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Journal of Chemical Information and Modeling, Volume 62
Volume 62, Number 1, January 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Haochuan Chen
, Han Liu
, Heying Feng, Haohao Fu
, Wensheng Cai
, Xueguang Shao
, Christophe Chipot
:
MLCV: Bridging Machine-Learning-Based Dimensionality Reduction and Free-Energy Calculation. 1-8 - Sakari Lätti
, Sanna P. Niinivehmas, Olli T. Pentikäinen
:
Sdfconf: A Novel, Flexible, and Robust Molecular Data Management Tool. 9-15 - Esther Heid
, Jiannan Liu, Andrea Aude, William H. Green Jr.
:
Influence of Template Size, Canonicalization, and Exclusivity for Retrosynthesis and Reaction Prediction Applications. 16-26 - Xianjin Xu
, Xiaoqin Zou
:
Predicting Protein-Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment. 27-39 - Felsis Angelene Daison
, Nitheeshkumar Kumar, Siranjeevi Balakrishnan, Kavyashree Venugopal, Sangamithra Elango, Pandian Sokkar
:
Molecular Dynamics Studies on the Bacterial Membrane Pore Formation by Small Molecule Antimicrobial Agents. 40-48 - Philipp Nicolas Depta
, Pavel Gurikov, Baldur Schroeter
, Attila Forgács, József Kalmár
, Geo Paul
, Leonardo Marchese
, Stefan Heinrich, Maksym Dosta:
DEM-Based Approach for the Modeling of Gelation and Its Application to Alginate. 49-70 - Kiyoshiro Okada
, Paul E. Brumby
, Kenji Yasuoka:
An Efficient Random Number Generation Method for Molecular Simulation. 71-78 - Jacob M. Litman, Chengwen Liu
, Pengyu Y. Ren
:
Atomic Polarizabilities for Interactive Dipole Induction Models. 79-87 - Hadrián Montes-Campos
, Jesús Carrete
, Sebastian Bichelmaier, Luis M. Varela
, Georg K. H. Madsen
:
A Differentiable Neural-Network Force Field for Ionic Liquids. 88-101 - Gamze Tanriver
, Gerald Monard
, Saron Catak
:
Impact of Deamidation on the Structure and Function of Antiapoptotic Bcl-xL. 102-115 - Austin Clyde, Stephanie Galanie, Daniel W. Kneller
, Heng Ma, Yadu N. Babuji, Ben Blaiszik, Alexander Brace, Thomas S. Brettin, Kyle Chard
, Ryan Chard, Leighton Coates
, Ian T. Foster, Darin Hauner, Vilmos Kertesz
, Neeraj Kumar
, Hyungro Lee, Zhuozhao Li
, André Merzky, Jurgen G. Schmidt, Li Tan, Mikhail Titov, Anda Trifan, Matteo Turilli
, Hubertus Van Dam
, Srinivas C. Chennubhotla, Shantenu Jha
, Andrey Kovalevsky
, Arvind Ramanathan
, Martha S. Head, Rick Stevens:
High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. 116-128 - Maryam Ghasemitarei
, Angela Privat-Maldonado
, Maksudbek Yusupov
, Shadi Rahnama, Annemie Bogaerts
, Mohammad Reza Ejtehadi
:
Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations. 129-141 - Samanta Makurat
, Zoe Cournia
, Janusz Rak
:
Inactive-to-Active Transition of Human Thymidine Kinase 1 Revealed by Molecular Dynamics Simulations. 142-149 - Jack A. Henderson
, Jana Shen
:
Exploring the pH- and Ligand-Dependent Flap Dynamics of Malarial Plasmepsin II. 150-158 - Jorge Enrique Hernández González
, Lucas N. Alberca, Yordanka Masforrol González, Osvaldo Reyes Acosta, Alan Talevi
, Emir Salas-Sarduy
:
Tetracycline Derivatives Inhibit Plasmodial Cysteine Protease Falcipain-2 through Binding to a Distal Allosteric Site. 159-175 - Beibei Wang
, Changqing Zhong, D. Peter Tieleman
:
Supramolecular Organization of SARS-CoV and SARS-CoV-2 Virions Revealed by Coarse-Grained Models of Intact Virus Envelopes. 176-186 - Juan Xie
, Shiwei Wang, Youjun Xu, Minghua Deng, Luhua Lai
:
Uncovering the Dominant Motion Modes of Allosteric Regulation Improves Allosteric Site Prediction. 187-195 - Bianca Fiorillo
, Silvia Marchianò, Federica Moraca
, Valentina Sepe, Adriana Carino, Pasquale Rapacciuolo
, Michele Biagioli, Vittorio Limongelli
, Angela Zampella, Bruno Catalanotti
, Stefano Fiorucci:
Discovery of Bile Acid Derivatives as Potent ACE2 Activators by Virtual Screening and Essential Dynamics. 196-209 - Gian Marco Elisi
, Laura Scalvini
, Alessio Lodola
, Marco Mor
, Silvia Rivara
:
Free-Energy Simulations Support a Lipophilic Binding Route for Melatonin Receptors. 210-222 - Zheng Zhao
, Lei Xie, Philip E. Bourne
:
Correction to "Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants". 223-224
Volume 62, Number 2, January 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Alejandro Varela-Rial
, Iain Maryanow, Maciej Majewski
, Stefan Doerr, Nikolai Schapin
, José Jiménez-Luna, Gianni De Fabritiis
:
PlayMolecule Glimpse: Understanding Protein-Ligand Property Predictions with Interpretable Neural Networks. 225-231 - Sorin Muraru
, Sebastian Muraru, Florentin Romeo Nitu
, Mariana Ionita
:
Recent Efforts and Milestones for Simulating Nucleic Acid FRET Experiments through Computational Methods. 232-239 - Jannis Born
, Tien Huynh, Astrid Stroobants
, Wendy D. Cornell, Matteo Manica
:
Active Site Sequence Representations of Human Kinases Outperform Full Sequence Representations for Affinity Prediction and Inhibitor Generation: 3D Effects in a 1D Model. 240-257 - Fei Zhu, Feifei Li, Lei Deng, Fanwang Meng, Zhongjie Liang
:
Protein Interaction Network Reconstruction with a Structural Gated Attention Deep Model by Incorporating Network Structure Information. 258-273 - José Jiménez-Luna
, Miha Skalic, Nils Weskamp
:
Benchmarking Molecular Feature Attribution Methods with Activity Cliffs. 274-283 - Mihaela D. Smilova
, Peter R. Curran, Chris J. Radoux, Frank von Delft, Jason C. Cole
, Anthony R. Bradley, Brian D. Marsden
:
Fragment Hotspot Mapping to Identify Selectivity-Determining Regions between Related Proteins. 284-294 - Christopher L. Hanselman, Xiangyu Yin
, David C. Miller
, Chrysanthos E. Gounaris
:
MatOpt: A Python Package for Nanomaterials Design Using Discrete Optimization. 295-308 - Solmaz Azimi
, Sheenam Khuttan
, Joe Z. Wu
, Rajat Kumar Pal
, Emilio Gallicchio
:
Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method. 309-323 - Bakar A. Hassan
, Jozafina Milicaj, Carlos Andres Ramirez-Mondragon, Yuk Yin Sham
, Erika A. Taylor
:
Ligand-Induced Conformational and Dynamical Changes in a GT-B Glycosyltransferase: Molecular Dynamics Simulations of Heptosyltransferase I Complexes. 324-339 - Dhanushka Weerakoon, Rodrigo J. Carbajo
, Leonardo De Maria
, Christian Tyrchan
, Hongtao Zhao
:
Impact of PROTAC Linker Plasticity on the Solution Conformations and Dissociation of the Ternary Complex. 340-349 - Kazuki Z. Yamamoto
, Nobuaki Yasuo
, Masakazu Sekijima
:
Screening for Inhibitors of Main Protease in SARS-CoV-2: In Silico and In Vitro Approach Avoiding Peptidyl Secondary Amides. 350-358 - Didac Martí, Carlos Alemán
, Jon Ainsley, Oscar Ahumada, Juan Torras
:
IgG1-b12-HIV-gp120 Interface in Solution: A Computational Study. 359-371 - Jun Chen, Hao Liu
, Xiaochen Cui, Zhengxin Li, Hai-Feng Chen
:
RNA-Specific Force Field Optimization with CMAP and Reweighting. 372-385 - Shu dong Wang
, Leif A. Eriksson
, Ru bo Zhang:
Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond. 386-398 - Narin Lawan
, Ruchanok Tinikul, Panida Surawatanawong, Adrian J. Mulholland
, Pimchai Chaiyen
:
QM/MM Molecular Modeling Reveals Mechanism Insights into Flavin Peroxide Formation in Bacterial Luciferase. 399-411 - Jiahui Chen
, Rui Wang
, Nancy Benovich Gilby, Guo-Wei Wei
:
Omicron Variant (B.1.1.529): Infectivity, Vaccine Breakthrough, and Antibody Resistance. 412-422
Volume 62, Number 3, February 2022
- Issue Editorial Masthead.
- Issue Publication Information.
- E. Adrian Henle
, Nickolas Gantzler
, Praveen K. Thallapally
, Xiaoli Z. Fern, Cory M. Simon
:
PoreMatMod.jl: Julia Package for in Silico Postsynthetic Modification of Crystal Structure Models. 423-432 - Yunsie Chung
, Florence H. Vermeire
, Haoyang Wu
, Pierre J. Walker
, Michael H. Abraham
, William H. Green Jr.
:
Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy. 433-446 - Tobias Harren
, Hans Matter
, Gerhard Hessler, Matthias Rarey
, Christoph Grebner
:
Interpretation of Structure-Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence. 447-462 - Jian Wang
, Nikolay V. Dokholyan
:
Yuel: Improving the Generalizability of Structure-Free Compound-Protein Interaction Prediction. 463-471 - Shuzhe Wang
, Kajo Krummenacher, Gregory A. Landrum
, Benjamin D. Sellers
, Paola Di Lello, Sarah J. Robinson, Bryan Martin, Jeffrey K. Holden, Jeffrey Y. K. Tom, Anastasia C. Murthy, Nataliya Popovych, Sereina Riniker
:
Incorporating NOE-Derived Distances in Conformer Generation of Cyclic Peptides with Distance Geometry. 472-485 - Dongping Li, Kexin Jiang, Dan Teng
, Zengrui Wu
, Weihua Li
, Yun Tang
, Rui Wang, Guixia Liu
:
Discovery of New Estrogen-Related Receptor α Agonists via a Combination Strategy Based on Shape Screening and Ensemble Docking. 486-497 - Wenyi Zhang, Jing Huang
:
EViS: An Enhanced Virtual Screening Approach Based on Pocket-Ligand Similarity. 498-510 - Alessandro Nicoli
, Andreas Dunkel
, Toni Giorgino, Chris de Graaf, Antonella Di Pizio
:
Classification Model for the Second Extracellular Loop of Class A GPCRs. 511-522 - Wenqing Li
, Jiabin Zhang, Li Guo, Qiantao Wang
:
Importance of Three-Body Problems and Protein-Protein Interactions in Proteolysis-Targeting Chimera Modeling: Insights from Molecular Dynamics Simulations. 523-532 - Francesc Sabanés Zariquiey
, Edgar Jacoby, Ann Vos, Herman W. T. van Vlijmen
, Gary Tresadern
, Jeremy N. Harvey
:
Divide and Conquer. Pocket-Opening Mixed-Solvent Simulations in the Perspective of Docking Virtual Screening Applications for Drug Discovery. 533-543 - Montserrat Penaloza-Amion
, Celso R. C. Rêgo
, Wolfgang Wenzel
:
Local Electronic Charge Transfer in the Helical Induction of Cis-Transoid Poly(4-carboxyphenyl)acetylene by Chiral Amines. 544-552 - Louis Bellmann
, Patrick Penner
, Marcus Gastreich, Matthias Rarey
:
Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs. 553-566 - Dalibor Trapl, Martin Krupicka
, Vladimír Visnovský, Jana Hozzová, Jaroslav Olha, Ales Krenek
, Vojtech Spiwok
:
Property Map Collective Variable as a Useful Tool for a Force Field Correction. 567-576 - Rory M. Crean, Christopher R. Pudney
, David K. Cole
, Marc van der Kamp
:
Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA. 577-590 - Samuel J. H. Gaughan
, Jonathan D. Hirst
, Anna K. Croft
, Christof M. Jäger
:
Effect of Oriented Electric Fields on Biologically Relevant Iron-Sulfur Clusters: Tuning Redox Reactivity for Catalysis. 591-601 - Josh Vincent Vermaas
, Christopher G. Mayne, Eric Shinn, Emad Tajkhorshid
:
Assembly and Analysis of Cell-Scale Membrane Envelopes. 602-617 - Debarati DasGupta
, Wallace K. B. Chan
, Heather A. Carlson
:
Computational Identification of Possible Allosteric Sites and Modulators of the SARS-CoV-2 Main Protease. 618-626 - Filip Fratev
:
R346K Mutation in the Mu Variant of SARS-CoV-2 Alters the Interactions with Monoclonal Antibodies from Class 2: A Free Energy Perturbation Study. 627-631 - Yijing Wang, Xinyi Li, Jingjing Wei, Xue Zhang, Yongjun Liu
:
Mechanism of Sugar Ring Contraction and Closure Catalyzed by UDP-d-apiose/UDP-d-xylose Synthase (UAXS). 632-646 - Qianzhen Shao
, Yaoyukun Jiang
, Zhongyue J. Yang
:
EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling. 647-655 - Xiaocong Wang
, Lihua Bie
, Jun Gao
:
Structural Insights into the Cofactor Role of Heparin/Heparan Sulfate in Binding between the SARS-CoV-2 Spike Protein and Host Angiotensin-Converting Enzyme II. 656-667 - Cecilia Chávez-García, Mikko Karttunen
:
Highly Similar Sequence and Structure Yet Different Biophysical Behavior: A Computational Study of Two Triosephosphate Isomerases. 668-677 - Damien Geslin, Alban Lepailleur
, Jean-Luc Manguin, Nhat-Vinh Vo, Jean Luc Lamotte
, Bertrand Cuissart, Ronan Bureau
:
Deciphering a Pharmacophore Network: A Case Study Using BCR-ABL Data. 678-691 - Xiao Li, Lun Zhang, Jing Xu, Chenyu Liu, Xiaojian Zhang, Amr Abbas Abdelmoneim, Qian Zhang, Jiaqi Ke, Yingnan Zhang, Lei Wang, Fan Yang, Cheng Luo
, Jia Jin
, Fei Ye
:
Identification, Synthesis, and Biological Evaluations of Potent Inhibitors Targeting Type I Protein Arginine Methyltransferases. 692-702 - Gary Tresadern
, Kanaka Tatikola, Javier Cabrera, Lingle Wang
, Robert Abel, Herman van Vlijmen
, Helena Geys:
The Impact of Experimental and Calculated Error on the Performance of Affinity Predictions. 703-717 - Gergely Zahoránszky-Köhalmi
, Vishal B. Siramshetty, Praveen Kumar, Manideep Gurumurthy, Busola Grillo, Biju Mathew, Dimitrios Metaxatos, Mark Backus, Tim Mierzwa, Reid Simon, Ivan Grishagin, Laura Brovold, Ewy A Mathé
, Matthew D. Hall
, Samuel G. Michael, Alexander G. Godfrey, Jordi Mestres
, Lars Juhl Jensen
, Tudor I. Oprea
:
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. 718-729 - Gen Li, Qing-Qing Dai, Guo-Bo Li
:
MeCOM: A Method for Comparing Three-Dimensional Metalloenzyme Active Sites. 730-739 - Hao Li, Yumeng Yan, Xuejun Zhao, Sheng-You Huang
:
Inclusion of Desolvation Energy into Protein-Protein Docking through Atomic Contact Potentials. 740-750 - (Withdrawn) Retraction of "Challenges in Predicting Aqueous Solubility of Organic Molecules Using the COSMO-RS Model". 751
Volume 62, Number 4, February 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Jade Young
, Neerja Garikipati, Jacob D. Durrant
:
BINANA 2: Characterizing Receptor/Ligand Interactions in Python and JavaScript. 753-760 - Eugene Lin
, Chieh-Hsin Lin, Hsien Yuan Lane:
De Novo Peptide and Protein Design Using Generative Adversarial Networks: An Update. 761-774 - Hiroko X. Kondo
, Masanori Fujii, Takuma Tanioka, Yusuke Kanematsu
, Takashi Yoshida, Yu Takano
:
Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket. 775-784 - Brajesh K. Rai
, Vishnu Sresht, Qingyi Yang
, Ray Unwalla
, Meihua Tu, Alan M. Mathiowetz, Gregory A. Bakken:
TorsionNet: A Deep Neural Network to Rapidly Predict Small-Molecule Torsional Energy Profiles with the Accuracy of Quantum Mechanics. 785-800 - Seung-gu Kang
, Joseph A. Morrone
, Jeffrey K. Weber, Wendy D. Cornell:
Analysis of Training and Seed Bias in Small Molecules Generated with a Conditional Graph-Based Variational Autoencoder─Insights for Practical AI-Driven Molecule Generation. 801-816 - André F. Oliveira
, Juarez L. F. Da Silva
, Marcos G. Quiles
:
Molecular Property Prediction and Molecular Design Using a Supervised Grammar Variational Autoencoder. 817-828 - Devon P. Holst, Pascal Friederich
, Alán Aspuru-Guzik
, Timothy P. Bender
:
Updated Calibrated Model for the Prediction of Molecular Frontier Orbital Energies and Its Application to Boron Subphthalocyanines. 829-840 - Jorge L. Castro Angamarca, Raúl Manzanilla Morillo, Thibault Terencio
:
Delta Chem: A New Geometric Approach of Porosity for Symmetric Porous Materials. 841-853 - Umesh B. Gadgoli
, Sunil Kumar Y. C.
, Deepak Kumar, Maya Pai, Sravani Pulya, Balaram Ghosh
, Onkar Prakash Kulkarni:
Estrogenic Activity of Tetrazole Derivatives Bearing Bisphenol Structures: Computational Studies, Synthesis, and In Vitro Assessment. 854-873 - Owen Madin
, Simon Boothroyd
, Richard A. Messerly, Josh Fass, John D. Chodera
, Michael R. Shirts
:
Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models. 874-889 - Lukas Krep
, Indu Sekhar Roy, Wassja A. Kopp, Felix Schmalz
, Can Huang, Kai Leonhard:
Efficient Reaction Space Exploration with ChemTraYzer-TAD. 890-902 - Ana Dreab
, Craig A. Bayse
:
Molecular Dynamics Simulations of Reduced and Oxidized TFIIIA Zinc Fingers Free and Interacting with 5S RNA. 903-913 - Soumendranath Bhakat
, Pär Söderhjelm:
Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems. 914-926 - Bianca Villavicencio
, Rodrigo Ligabue-Braun
, Hugo Verli
:
Structural Characteristics of Glycocins: Unraveling the Role of S-Linked Carbohydrates and Other Structural Elements. 927-935 - Baocai Ma
, Zuoheng Zhang, Yan Li, Xubo Lin
, Ning Gu
:
Evaluation of Interactions between SARS-CoV-2 RBD and Full-Length ACE2 with Coarse-Grained Molecular Dynamics Simulations. 936-944 - Naiá Porã Santos, Lucianna Helene Santos
, Mariana Torquato Quezado de Magalhães
, Jian Lei, Rolf Hilgenfeld
, Rafaela Salgado Ferreira
, Lucas Bleicher
:
Characterization of an Allosteric Pocket in Zika Virus NS2B-NS3 Protease. 945-957 - Cecilia Chávez-García, Jérôme Hénin, Mikko Karttunen
:
Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2. 958-970 - Yaoxi Chen
, Quan Chen, Haiyan Liu
:
DEPACT and PACMatch: A Workflow of Designing De Novo Protein Pockets to Bind Small Molecules. 971-985 - Giuseppe Licari
, Sepehr Dehghani-Ghahnaviyeh, Emad Tajkhorshid
:
Membrane Mixer: A Toolkit for Efficient Shuffling of Lipids in Heterogeneous Biological Membranes. 986-996 - Farideh Badichi Akher
, Abdolkarim Farrokhzadeh
, Neil Ravenscroft
, Michelle M. Kuttel
:
Deciphering the Mechanism of Binding Selectivity of Chlorofluoroacetamide-Based Covalent Inhibitors toward L858R/T790M Resistance Mutation. 997-1013 - Ilaria Salutari
, Amedeo Caflisch
:
Dynamics of the Histone Acetyltransferase Lysine-Rich Loop in the Catalytic Core of the CREB-Binding Protein. 1014-1024 - Shalini Yadav
, Sason Shaik
, Shakir Ali Siddiqui
, Surajit Kalita
, Kshatresh Dutta Dubey
:
Local Electric Fields Dictate Function: The Different Product Selectivities Observed for Fatty Acid Oxidation by Two Deceptively Very Similar P450-Peroxygenases OleT and BSβ. 1025-1035 - Irina D. Pogozheva
, Grant A. Armstrong
, Lingyang Kong
, Timothy J. Hartnagel
, Carly A. Carpino
, Stephen E. Gee
, Danielle M. Picarello
, Amanda S. Rubin
, Jumin Lee
, Soohyung Park
, Andrei L. Lomize
, Wonpil Im
:
Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes. 1036-1051 - Yao Chi Chen, Yu-Hsien Chen
, Jon D. Wright, Carmay Lim
:
PPI-HotspotDB: Database of Protein-Protein Interaction Hot Spots. 1052-1060 - Anne Labarre
, Julia K. Stille, Mihai Burai Patrascu, Andrew Martins, Joshua Pottel
, Nicolas Moitessier
:
Docking Ligands into Flexible and Solvated Macromolecules. 8. Forming New Bonds─Challenges and Opportunities. 1061-1077 - Suqing Zheng, Lei Wang, Jun Xiong, Guang Liang, Yong Xu, Fu Lin
:
Consensus Prediction of Human Gut Microbiota-Mediated Metabolism Susceptibility for Small Molecules by Machine Learning, Structural Alerts, and Dietary Compounds-Based Average Similarity Methods. 1078-1099 - Sami T. Kurkinen
, Jukka V. Lehtonen
, Olli T. Pentikäinen
, Pekka A. Postila
:
Optimization of Cavity-Based Negative Images to Boost Docking Enrichment in Virtual Screening. 1100-1112 - Daniela Trisciuzzi, Lydia Siragusa
, Massimo Baroni, Ida Autiero
, Orazio Nicolotti
, Gabriele Cruciani
:
Getting Insights into Structural and Energetic Properties of Reciprocal Peptide-Protein Interactions. 1113-1125 - Anu R. Melge, Shraddha Parate
, Keechilat Pavithran
, Manzoor Koyakutty, C. Gopi Mohan
:
Discovery of Anticancer Hybrid Molecules by Supervised Machine Learning Models and in Vitro Validation in Drug Resistant Chronic Myeloid Leukemia Cells. 1126-1146
Volume 62, Number 5, March 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Raphaël Robidas
, Claude Y. Legault
:
CalcUS: An Open-Source Quantum Chemistry Web Platform. 1147-1153 - Alexander von Wedelstedt
, Gunther Goebel
, Grit Kalies:
MOF-VR: A Virtual Reality Program for Performing and Visualizing Immersive Molecular Dynamics Simulations of Guest Molecules in Metal-Organic Frameworks. 1154-1159 - Yuriy A. Abramov
, Guangxu Sun, Qun Zeng:
Emerging Landscape of Computational Modeling in Pharmaceutical Development. 1160-1171 - Vytautas Gapsys
, David F. Hahn, Gary Tresadern
, David L. Mobley
, Markus Rampp, Bert L. de Groot
:
Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design. 1172-1177 - Kate A. Stafford, Brandon M. Anderson, Jon Sorenson
, Henry van den Bedem
:
AtomNet PoseRanker: Enriching Ligand Pose Quality for Dynamic Proteins in Virtual High-Throughput Screens. 1178-1189 - Hyunsoo Park
, Yeonghun Kang
, Wonyoung Choe
, Jihan Kim
:
Mining Insights on Metal-Organic Framework Synthesis from Scientific Literature Texts. 1190-1198 - Michael Moret, Francesca Grisoni
, Paul Katzberger, Gisbert Schneider
:
Perplexity-Based Molecule Ranking and Bias Estimation of Chemical Language Models. 1199-1206 - Taketomo Isazawa
, Jacqueline M. Cole
:
Single Model for Organic and Inorganic Chemical Named Entity Recognition in ChemDataExtractor. 1207-1213 - Jaime Carracedo-Cosme
, Carlos Romero-Muñiz
, Pablo Pou, Rubén Pérez
:
QUAM-AFM: A Free Database for Molecular Identification by Atomic Force Microscopy. 1214-1223 - Simon Cross
, Gabriele Cruciani
:
FragExplorer: GRID-Based Fragment Growing and Replacement. 1224-1235 - Luca Andrade
, Aline Albuquerque, Andrielly Santos-Costa
, Disraeli Vasconcelos, Wilson Savino, Geraldo Rodrigues Sartori
, João Herminio Martins Da Silva
:
Investigation of Unprecedented Sites and Proposition of New Ligands for Programmed Cell Death Protein I through Molecular Dynamics with Probes and Virtual Screening. 1236-1248 - Hongmao Sun
, Nathan P. Coussens, Carina Danchik, Leah M. Wachsmuth, Mark J. Henderson
, Samarjit Patnaik
, Matthew D. Hall
, Ashley L. Molinaro, Dayle A. Daines, Min Shen:
Discovery of Small-Molecule VapC1 Nuclease Inhibitors by Virtual Screening and Scaffold Hopping from an Atomic Structure Revealing Protein-Protein Interactions with a Native VapB1 Inhibitor. 1249-1258 - Javier L. Baylon
, Oleg Ursu
, Anja Muzdalo, Anne Mai Wassermann, Gregory L. Adams
, Martin Spale, Petr Mejzlík, Anna Gromek, Viktor Pisarenko, Dzianis Hancharyk, Esteban Jenkins, David Bednar, Charlie Chang, Kamila Clarova, Meir Glick, Danny A. Bitton
:
PepSeA: Peptide Sequence Alignment and Visualization Tools to Enable Lead Optimization. 1259-1267 - Alexander Zech
, Timur Bazhirov
:
CateCom: A Practical Data-Centric Approach to Categorization of Computational Models. 1268-1281 - Dharmeshkumar Patel
, Stephanie L. Haag
, Jagdish Suresh Patel
, F. Marty Ytreberg, Matthew T. Bernards
:
Paired Simulations and Experimental Investigations into the Calcium-Dependent Conformation of Albumin. 1282-1293 - Mohamed Marzouk Sobeh
, Akio Kitao
:
Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM. 1294-1307 - Penglei Wang
, Shuangjia Zheng
, Yize Jiang, Chengtao Li, Junhong Liu, Chang Wen, Atanas Patronov, Dahong Qian, Hongming Chen
, Yuedong Yang
:
Structure-Aware Multimodal Deep Learning for Drug-Protein Interaction Prediction. 1308-1317 - Islem Hammami, Géraldine Farjot, Mikaël Naveau, Audrey Rousseaud, Thierry Prangé, Ira Katz, Nathalie Colloc'h
:
Method for the Identification of Potentially Bioactive Argon Binding Sites in Protein Families. 1318-1327 - Masahiko Taguchi
, Ryo Oyama, Masahiro Kaneso, Shigehiko Hayashi
:
Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease. 1328-1344 - Narod Kebabci
, Ahmet Can Timucin
, Emel Timuçin
:
Toward Compilation of Balanced Protein Stability Data Sets: Flattening the ΔΔG Curve through Systematic Enrichment. 1345-1355
Volume 62, Number 6, March 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Shoichi Ishida
, Kei Terayama
, Ryosuke Kojima
, Kiyosei Takasu, Yasushi Okuno:
AI-Driven Synthetic Route Design Incorporated with Retrosynthesis Knowledge. 1357-1367 - Jinning Shao, Yue Liu, Jiaqi Yan, Ze-Yi Yan, Yangyang Wu, Zhongying Ru
, Jia-Yu Liao
, Xiaoye Miao, Linghui Qian
:
Prediction of Maximum Absorption Wavelength Using Deep Neural Networks. 1368-1375 - Jieyu Lu, Yingkai Zhang
:
Unified Deep Learning Model for Multitask Reaction Predictions with Explanation. 1376-1387 - Giovanni Bolcato, Esther Heid
, Jonas Boström
:
On the Value of Using 3D Shape and Electrostatic Similarities in Deep Generative Methods. 1388-1398 - Chuan Li, Jiangting Liu
, Jianfang Chen, Yuan Yuan, Jin Yu
, Qiaolin Gou, Yanzhi Guo, Xuemei Pu
:
An Interpretable Convolutional Neural Network Framework for Analyzing Molecular Dynamics Trajectories: a Case Study on Functional States for G-Protein-Coupled Receptors. 1399-1410 - Teresa Maria Creanza
, Giuseppe Lamanna, Pietro Delre
, Marialessandra Contino
, Nicola Corriero, Michele Saviano
, Giuseppe Felice Mangiatordi
, Nicola Ancona
:
DeLA-Drug: A Deep Learning Algorithm for Automated Design of Druglike Analogues. 1411-1424 - Corentin Bedart
, Nicolas Renault
, Philippe Chavatte, Adeline Porcherie, Abderrahim Lachgar, Monique Capron, Amaury Farce
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SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations. 1425-1436 - Pradip Bera, Abhishek Aher, Paula Brandao, Utsab Debnath, Varun Dewaker, Sunil Kr. Manna, Abhimanyu Jana, Chandana Pramanik, Basudev Mandal, Pulakesh Bera
:
Instigating the In Vitro Anticancer Activity of New Pyridine-Thiazole-Based Co(III), Mn(II), and Ni(II) Complexes: Synthesis, Structure, DFT, Docking, and MD Simulation Studies. 1437-1457 - Ellen E. Guest
, Luis F. Cervantes, Stephen D. Pickett
, Charles L. Brooks III
, Jonathan D. Hirst
:
Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4. 1458-1470 - Carlos E. S. Bernardes
:
DLPGEN: Preparing Molecular Dynamics Simulations with Support for Polarizable Force Fields. 1471-1478 - Jonah Z. Vilseck
, Luis F. Cervantes, Ryan L. Hayes, Charles L. Brooks III
:
Optimizing Multisite λ-Dynamics Throughput with Charge Renormalization. 1479-1488 - Noam Morningstar-Kywi
, Kaichen Wang, Thomas R. Asbell, Zhaohui Wang, Jason B. Giles, Jiawei Lai, Dab Brill, Brian T. Sutch, Ian S. Haworth
:
Prediction of Water Distributions and Displacement at Protein-Ligand Interfaces. 1489-1497 - Kowit Hengphasatporn
, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont
, Warinthorn Chavasiri, Peerapat Visitchanakun, Asada Leelahavanichkul, Wattamon Paunrat, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol
, Supot Hannongbua
, Yasuteru Shigeta
:
Halogenated Baicalein as a Promising Antiviral Agent toward SARS-CoV-2 Main Protease. 1498-1509 - Roberto López
, Natalia Díaz
, Evelio Francisco
, Ángel Martín Pendás
, Dimas Suárez
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QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach. 1510-1524 - Steven R. Bowers, Dmitri K. Klimov
, Christopher Lockhart
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Mechanisms of Binding of Antimicrobial Peptide PGLa to DMPC/DMPG Membrane. 1525-1537 - Alexander Neumann
, Isaac Attah, Haneen Al-Hroub, Vigneshwaran Namasivayam
, Christa E. Müller
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Discovery of P2Y2 Receptor Antagonist Scaffolds through Virtual High-Throughput Screening. 1538-1549 - C. Johan van der Westhuizen
, André Stander, Darren L. Riley
, Jenny-Lee Panayides
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Discovery of Novel Acetylcholinesterase Inhibitors by Virtual Screening, In Vitro Screening, and Molecular Dynamics Simulations. 1550-1572 - Janez Konc
, Samo Lesnik, Blaz Skrlj, Matej Sova, Matic Proj
, Damijan Knez
, Stanislav Gobec
, Dusanka Janezic
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ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison. 1573-1584 - Amol Tagad
, Reman Kumar Singh
, G. Naresh Patwari
:
Binary Matrix Method to Enumerate, Hierarchically Order, and Structurally Classify Peptide Aggregation. 1585-1594
Volume 62, Number 7, April 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Hugo Schweke, Marie-Hélène Mucchielli, Nicolas Chevrollier, Simon Gosset, Anne Lopes
:
SURFMAP: A Software for Mapping in Two Dimensions Protein Surface Features. 1595-1601 - Amr H. Mahmoud, Matthew Masters, Soo Jung Lee, Markus A. Lill
:
Accurate Sampling of Macromolecular Conformations Using Adaptive Deep Learning and Coarse-Grained Representation. 1602-1617 - Gonzalo Cerruela García
, José Manuel Cuevas-Muñoz
, Nicolás García-Pedrajas:
Graph-Based Feature Selection Approach for Molecular Activity Prediction. 1618-1632 - Miao Zhu, Jacqueline M. Cole
:
PDFDataExtractor: A Tool for Reading Scientific Text and Interpreting Metadata from the Typeset Literature in the Portable Document Format. 1633-1643 - Patrick Penner
, Wolfgang Guba, Robert Schmidt
, Agnes Meyder
, Martin Stahl, Matthias Rarey
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The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare. 1644-1653 - Yi Hua, Xiaobao Fang, Guomeng Xing, Yuan Xu, Li Liang, Chenglong Deng, Xiaowen Dai, Haichun Liu, Tao Lu, Yanmin Zhang
, Yadong Chen
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Effective Reaction-Based De Novo Strategy for Kinase Targets: A Case Study on MERTK Inhibitors. 1654-1668 - Bhagyesh Varvdekar, Akshay Prabhakant, Marimuthu Krishnan
:
Response of Terahertz Protein Vibrations to Ligand Binding: Calmodulin-Peptide Complexes as a Case Study. 1669-1679 - Bongkochawan Pakamwong
, Paptawan Thongdee
, Bundit Kamsri
, Naruedon Phusi
, Pharit Kamsri
, Auradee Punkvang
, Sombat Ketrat
, Patchreenart Saparpakorn
, Supa Hannongbua
, Kanchiyaphat Ariyachaokun
, Khomson Suttisintong
, Sanya Sureram
, Prasat Kittakoop
, Poonpilas Hongmanee
, Pitak Santanirand, James Spencer
, Adrian J. Mulholland
, Pornpan Pungpo
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Identification of Potent DNA Gyrase Inhibitors Active against Mycobacterium tuberculosis. 1680-1690 - Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmüller
, Bert L. de Groot
, Vytautas Gapsys
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GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design. 1691-1711 - Jiming Chen
, David C. Nelson, Diwakar Shukla
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Activation Mechanism of Strigolactone Receptors and Its Impact on Ligand Selectivity between Host and Parasitic Plants. 1712-1722 - Osvaldo Burastero
, Marisol Cabrera, Elias D. López
, Lucas A. Defelipe
, Juan Pablo Arcon
, Rosario Durán
, Marcelo A. Marti
, Adrian Gustavo Turjanski
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Specificity and Reactivity of Mycobacterium tuberculosis Serine/Threonine Kinases PknG and PknB. 1723-1733 - Kang Ding, Shiqiu Yin, Zhongwei Li, Shiju Jiang, Yang Yang, Wenbiao Zhou, Yingsheng Zhang
, Bo Huang
:
Observing Noncovalent Interactions in Experimental Electron Density for Macromolecular Systems: A Novel Perspective for Protein-Ligand Interaction Research. 1734-1743 - Nabeel Ahmad
, Anamika Singh, Akshita Gupta, Pradeep Pant
, Tej P. Singh, Sujata Sharma, Pradeep Sharma
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Discovery of the Lead Molecules Targeting the First Step of the Histidine Biosynthesis Pathway of Acinetobacter baumannii. 1744-1759 - Huayuan Tang, Yunxiang Sun
, Feng Ding
:
Hydrophobic/Hydrophilic Ratio of Amphiphilic Helix Mimetics Determines the Effects on Islet Amyloid Polypeptide Aggregation. 1760-1770 - Sungbo Hwang
, Seung-Hwa Baek, Daeui Park
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Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. 1771-1782 - Anup P. Challa
, Xin Hu, Ya-Qin Zhang, Jeffrey Hymes, Bret D. Wallace, Surendra Karavadhi, Hongmao Sun
, Samarjit Patnaik
, Matthew D. Hall
, Min Shen
:
Virtual Screening for the Discovery of Microbiome β-Glucuronidase Inhibitors to Alleviate Cancer Drug Toxicity. 1783-1793 - Lu-Xing Zhang, He Yan, Yan Liu, Jian Xu, Jiangning Song
, Dong-Jun Yu
:
Enhancing Characteristic Gene Selection and Tumor Classification by the Robust Laplacian Supervised Discriminative Sparse PCA. 1794-1807
Volume 62, Number 8, April 2022
- Vineeth R. Chelur, U. Deva Priyakumar
:
BiRDS - Binding Residue Detection from Protein Sequences Using Deep ResNets. 1809-1818 - Andrew T. McNutt
, David Ryan Koes
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Improving ΔΔG Predictions with a Multitask Convolutional Siamese Network. 1819-1829 - Xudong Zhang, Jun Mao, Min Wei, Yifei Qi
, John Z. H. Zhang
:
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models. 1830-1839 - Dongdong Zhang, Song Xia, Yingkai Zhang
:
Accurate Prediction of Aqueous Free Solvation Energies Using 3D Atomic Feature-Based Graph Neural Network with Transfer Learning. 1840-1848 - Christophe Molina
, Lilia Ait-Ouarab, Hervé Minoux:
Isometric Stratified Ensembles: A Partial and Incremental Adaptive Applicability Domain and Consensus-Based Classification Strategy for Highly Imbalanced Data Sets with Application to Colloidal Aggregation. 1849-1862 - Alba Fombona-Pascual
, Javier Fombona
, Rubén Vicente
:
Augmented Reality, a Review of a Way to Represent and Manipulate 3D Chemical Structures. 1863-1872 - Zhen Wang, Haitao Ji
:
Characterization of Hydrophilic α-Helical Hot Spots on the Protein-Protein Interaction Interfaces for the Design of α-Helix Mimetics. 1873-1890 - She Zhang
, Jeffrey P. Thompson
, Junchao Xia, Anthony T. Bogetti
, Forrest York, A. Geoffrey Skillman, Lillian T. Chong
, David N. LeBard
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Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories. 1891-1904 - Pieter H. Bos
, Evelyne M. Houang, Fabio Ranalli, Abba E. Leffler, Nicholas A. Boyles, Volker A. Eyrich, Yuval Luria, Dana Katz, Haifeng Tang
, Robert Abel, Sathesh Bhat
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AutoDesigner, a De Novo Design Algorithm for Rapidly Exploring Large Chemical Space for Lead Optimization: Application to the Design and Synthesis of d-Amino Acid Oxidase Inhibitors. 1905-1915 - Srikanta Sen, Munna Sarkar
:
Insights on Rigidity and Flexibility at the Global and Local Levels of Protein Structures and Their Roles in Homologous Psychrophilic, Mesophilic, and Thermophilic Proteins: A Computational Study. 1916-1932 - Xiaoting Liu, Ji-Long Zhang
:
In Silico Investigation on KAR Signaling Reveals the Significant Dynamic Change of Its Receptor's Structure. 1933-1941 - Souvik Mondal
, Krishna Prasad Ghanta
, Sanjoy Bandyopadhyay
:
Dynamic Heterogeneity at the Interface of an Intrinsically Disordered Peptide. 1942-1955 - Gennady M. Verkhivker
, Steve Agajanian, Ryan Kassab, Keerthi Krishnan:
Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike Variants. 1956-1978 - Phillip W. Gingrich, Justin B. Siegel, Dean J. Tantillo
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Assessing Alkene Reactivity toward Cytochrome P450-Mediated Epoxidation through Localized Descriptors and Regression Modeling. 1979-1987 - Peng Gao
, Miao Xu, Qi Zhang
, Catherine Z. Chen, Hui Guo, Yihong Ye, Wei Zheng
, Min Shen
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Graph Convolutional Network-Based Screening Strategy for Rapid Identification of SARS-CoV-2 Cell-Entry Inhibitors. 1988-1997 - Juhi Dutta
, Akshay Kumar Sahu, Abhijeet S. Bhadauria, Himansu S. Biswal
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Carbon-Centered Hydrogen Bonds in Proteins. 1998-2008
Volume 62, Number 9, May 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Matthias Rarey
, Marc C. Nicklaus
, Wendy Warr
:
Special Issue on Reaction Informatics and Chemical Space. 2009-2010 - Pierre Baldi
:
Call for a Public Open Database of All Chemical Reactions. 2011-2014 - Timur Gimadiev, Ramil I. Nugmanov, Aigul Khakimova, Adeliya Fatykhova, Timur I. Madzhidov, Pavel Sidorov, Alexandre Varnek:
CGRdb2.0: A Python Database Management System for Molecules, Reactions, and Chemical Data. 2015-2020 - Wendy A. Warr
, Marc C. Nicklaus
, Christos A. Nicolaou
, Matthias Rarey
:
Exploration of Ultralarge Compound Collections for Drug Discovery. 2021-2034 - Jiang Guo
, A. Santiago Ibanez-Lopez, Hanyu Gao
, Victor Quach, Connor W. Coley
, Klavs F. Jensen
, Regina Barzilay:
Automated Chemical Reaction Extraction from Scientific Literature. 2035-2045 - Vendy Fialková, Jiaxi Zhao, Kostas Papadopoulos
, Ola Engkvist
, Esben Jannik Bjerrum
, Thierry Kogej, Atanas Patronov
:
LibINVENT: Reaction-based Generative Scaffold Decoration for in Silico Library Design. 2046-2063 - Viraj Bagal, Rishal Aggarwal, P. K. Vinod
, U. Deva Priyakumar
:
MolGPT: Molecular Generation Using a Transformer-Decoder Model. 2064-2076 - Alexe L. Haywood
, Joseph Redshaw, Magnus W. D. Hanson-Heine
, Adam Taylor
, Alex Brown
, Andrew M. Mason, Thomas Gärtner, Jonathan D. Hirst
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Kernel Methods for Predicting Yields of Chemical Reactions. 2077-2092 - Rocío Mercado, Esben Jannik Bjerrum
, Ola Engkvist
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Exploring Graph Traversal Algorithms in Graph-Based Molecular Generation. 2093-2100 - Esther Heid
, William H. Green Jr.
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Machine Learning of Reaction Properties via Learned Representations of the Condensed Graph of Reaction. 2101-2110 - Philipp Seidl
, Philipp Renz
, Natalia Dyubankova, Paulo Neves
, Jonas Verhoeven, Jörg K. Wegner
, Marwin H. S. Segler
, Sepp Hochreiter, Günter Klambauer:
Improving Few- and Zero-Shot Reaction Template Prediction Using Modern Hopfield Networks. 2111-2120 - Mohammadamin Tavakoli, Aaron Mood, David Van Vranken, Pierre Baldi
:
Quantum Mechanics and Machine Learning Synergies: Graph Attention Neural Networks to Predict Chemical Reactivity. 2121-2132 - Robert Schmidt
, Raphael Klein
, Matthias Rarey
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Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces. 2133-2150 - Yuliana Zabolotna
, Dmitriy M. Volochnyuk, Sergey V. Ryabukhin
, Kostiantyn Gavrylenko, Dragos Horvath
, Olga Klimchuk, Oleksandr Oksiuta, Gilles Marcou
, Alexandre Varnek
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SynthI: A New Open-Source Tool for Synthon-Based Library Design. 2151-2163 - Peter Ertl
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Magic Rings: Navigation in the Ring Chemical Space Guided by the Bioactive Rings. 2164-2170 - Yuliana Zabolotna
, Dmitriy M. Volochnyuk, Sergey V. Ryabukhin
, Dragos Horvath
, Konstantin S. Gavrilenko, Gilles Marcou
, Yurii S. Moroz, Oleksandr Oksiuta, Alexandre Varnek
:
A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry. 2171-2185 - Timothy B. Dunn, Gustavo de M. Seabra
, Taewon David Kim, K. Eurídice Juárez-Mercado
, Chenglong Li, José L. Medina-Franco
, Ramón Alain Miranda-Quintana
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Diversity and Chemical Library Networks of Large Data Sets. 2186-2201 - Joel Wahl
, Thomas Sander:
Fully Automated Creation of Virtual Chemical Fragment Spaces Using the Open-Source Library OpenChemLib. 2202-2211 - Kazuma Kaitoh
, Yoshihiro Yamanishi
:
Scaffold-Retained Structure Generator to Exhaustively Create Molecules in an Arbitrary Chemical Space. 2212-2225 - Gergely Zahoránszky-Köhalmi, Nikita Lysov, Ilia Vorontcov, Jeffrey Wang, Jeyaraman Soundararajan, Dimitrios Metaxotos, Biju Mathew, Rafat Sarosh, Samuel G. Michael, Alexander G. Godfrey:
Algorithm for the Pruning of Synthesis Graphs. 2226-2238 - Hongyao Zhu
, Timothy L. Foley, Justin I. Montgomery, Robert V. Stanton:
Understanding Data Noise and Uncertainty through Analysis of Replicate Samples in DNA-Encoded Library Selection. 2239-2247 - Dongming Lan, Shu Li
, Wei Tang, Zexin Zhao
, Mupeng Luo
, Shuguang Yuan, Jun Xu
, Yonghua Wang
:
Glycerol is Released from a New Path in MGL Lipase Catalytic Process. 2248-2256
Volume 62, Number 10, May 2022
- Issue Editorial Masthead.
- Issue Publication Information.
- Timothy Cholko
, Shivansh Kaushik
, Kingsley Y. Wu
, Ruben Montes
, Chia-en A. Chang
:
GeomBD3: Brownian Dynamics Simulation Software for Biological and Engineered Systems. 2257-2263 - Steven R. Shave
, Nhan T. Pham
, Manfred Auer
:
CLAffinity: A Software Tool for Identification of Optimum Ligand Affinity for Competition-Based Primary Screens. 2264-2268 - Weixin Xie, Fanhao Wang, Yibo Li, Luhua Lai
, Jianfeng Pei
:
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models. 2269-2279 - Thomas E. Hadfield
, Fergus Imrie
, Andy Merritt
, Kristian Birchall, Charlotte M. Deane
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Incorporating Target-Specific Pharmacophoric Information into Deep Generative Models for Fragment Elaboration. 2280-2292 - Cheng-Hao Liu
, Maksym Korablyov, Stanislaw Jastrzebski, Pawel Wlodarczyk-Pruszynski, Yoshua Bengio, Marwin H. S. Segler
:
RetroGNN: Fast Estimation of Synthesizability for Virtual Screening and De Novo Design by Learning from Slow Retrosynthesis Software. 2293-2300 - Heesung Shim
, Hyojin Kim
, Jonathan E. Allen
, Heike Wulff
:
Pose Classification Using Three-Dimensional Atomic Structure-Based Neural Networks Applied to Ion Channel-Ligand Docking. 2301-2315 - Katherine S. Lim
, Andrew G. Reidenbach, Bruce K. Hua
, Jeremy W. Mason, Christopher J. Gerry
, Paul A. Clemons, Connor W. Coley
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Machine Learning on DNA-Encoded Library Count Data Using an Uncertainty-Aware Probabilistic Loss Function. 2316-2331 - Alexander P. Shevchenko
, Michail I. Smolkov
, Junjie Wang, Vladislav A. Blatov
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Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds. 2332-2340 - Junhui Park
, Gaeun Sung
, Seunghyun Lee
, Seungho Kang
, Chunkyun Park
:
ACGCN: Graph Convolutional Networks for Activity Cliff Prediction between Matched Molecular Pairs. 2341-2351 - Lin Ji
, Yue Li, Jie Wang, An Ning
, Naixin Zhang, Shengyao Liang, Jiyun He, Tianyu Zhang, Zexing Qu
, Jiali Gao
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Community Reaction Network Reduction for Constructing a Coarse-Grained Representation of Combustion Reaction Mechanisms. 2352-2364 - Thi Chinh Ngo
, Duy Quang Dao
, Tam Van-Thanh Mai
, Thi Le Anh Nguyen
, Lam Kim Huynh
:
On The Radical Scavenging and DNA Repairing Activities by Natural Oxygenated Diterpenoids: Theoretical Insights. 2365-2377 - Dewi Yokelson
, Nikolay V. Tkachenko
, Robert Robey, Ying Wai Li, Pavel A. Dub
:
Performance Analysis of CP2K Code for Ab Initio Molecular Dynamics on CPUs and GPUs. 2378-2386 - Narges Cheshmazar, Salar Hemmati
, Maryam Hamzeh-Mivehroud, Babak Sokouti
, Matthes Zessin, Mike Schutkowski
, Wolfgang Sippl
, Hojjatollah Nozad Charoudeh, Siavoush Dastmalchi
:
Development of New Inhibitors of HDAC1-3 Enzymes Aided by In Silico Design Strategies. 2387-2397 - Wei-Hua Yang, Ya-Meng Li, Jian-Xiang Bi, Rao Huang
, Gui-Fang Shao
, Tian-E. Fan, Tun-Dong Liu, Yu-Hua Wen
:
An Improved Self-Adaptive Differential Evolution with the Neighborhood Search Algorithm for Global Optimization of Bimetallic Clusters. 2398-2408 - Vikram Dalal
, Dasantila Golemi-Kotra, Pravindra Kumar
:
Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of Staphylococcus aureus. 2409-2420 - Xiu Li, Shiying Zhou, Xubo Lin
:
Molecular View on the Impact of DHA Molecules on the Physical Properties of a Model Cell Membrane. 2421-2431 - Diego Moreno Martinez
, Dominique Guillaumont
, Philippe Guilbaud
:
Force Field Parameterization of Actinyl Molecular Cations Using the 12-6-4 Model. 2432-2445 - Valery R. Polyakov
, Vadim Alexandrov, Andreas Maderna, Krishna Bajjuri, Xiaofan Li
, Sihong Zhou:
Indexing Ultrafast Shape-Based Descriptors in MongoDB to Identify TLR4 Pathway Agonists. 2446-2455 - Sehr Naseem-Khan
, Madison B. Berger
, Emmett M. Leddin
, Yazdan Maghsoud
, G. Andrés Cisneros
:
Impact of Remdesivir Incorporation along the Primer Strand on SARS-CoV-2 RNA-Dependent RNA Polymerase. 2456-2465 - Leonardo F. Serafim, Vindi M. Jayasinghe-Arachchige, Lukun Wang, Rajeev Prabhakar
:
Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses. 2466-2480 - Carmen Domene
, Leonardo Darré
, Victoria Oakes, Saul Gonzalez-Resines:
A Potential Route of Capsaicin to Its Binding Site in the TRPV1 Ion Channel. 2481-2489 - Mert Golcuk, Aysima Hacisuleyman, Sema Zeynep Yilmaz, Elhan Taka, Ahmet Yildiz, Mert Gur:
SARS-CoV-2 Delta Variant Decreases Nanobody Binding and ACE2 Blocking Effectivity. 2490-2498 - Xiaolin Pan
, Hao Wang, Yueqing Zhang, Xingyu Wang, Cuiyu Li, Changge Ji
, John Z. H. Zhang
:
AA-Score: a New Scoring Function Based on Amino Acid-Specific Interaction for Molecular Docking. 2499-2509 - Luís M. C. Teixeira
, João T. S. Coimbra
, Maria João Ramos
, Pedro Alexandrino Fernandes
:
Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV-2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19 Pandemic. 2510-2521 - Sukanya Mozumder, Aritra Bej
, Jayati Sengupta
:
Ligand-Dependent Modulation of the Dynamics of Intracellular Loops Dictates Functional Selectivity of 5-HT2AR. 2522-2537 - Qiaojing Huang
, Luhua Lai
, Zhirong Liu
:
Quantitative Analysis of Dynamic Allostery. 2538-2549 - Nuno F. B. Oliveira
, Miguel Machuqueiro
:
Novel US-CpHMD Protocol to Study the Protonation-Dependent Mechanism of the ATP/ADP Carrier. 2550-2560 - Shunzhou Wan
, Agastya P. Bhati
, David W. Wright
, Ian D. Wall, Alan P. Graves, Darren V. S. Green, Peter V. Coveney
:
Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors. 2561-2570 - Nemanja Djokovic
, Dusan Ruzic
, Minna Rahnasto-Rilla, Tatjana Srdic-Rajic
, Maija Lahtela-Kakkonen
, Katarina Nikolic
:
Expanding the Accessible Chemical Space of SIRT2 Inhibitors through Exploration of Binding Pocket Dynamics. 2571-2585 - Xavier Chee Wezen
, Aneesh Chandran, Rohan Sakariah Eapen
, Elaine Waters, Laura Bricio-Moreno, Tommaso Tosi, Stephen Dolan, Charlotte Millership, Aras Kadioglu, Angelika Gründling, Laura S. Itzhaki
, Martin Welch, Taufiq Rahman
:
Structure-Based Discovery of Lipoteichoic Acid Synthase Inhibitors. 2586-2599 - Dominique Sydow
, Eva Aßmann
, Albert J. Kooistra
, Friedrich Rippmann
, Andrea Volkamer
:
KiSSim: Predicting Off-Targets from Structural Similarities in the Kinome. 2600-2616 - Qushuo Chen, Changyan Yang, Yihao Xie, Yuqiang Wang, Xiaoxu Li, Kairong Wang
, Jinqi Huang
, Wenjin Yan
:
GM-Pep: A High Efficiency Strategy to De Novo Design Functional Peptide Sequences. 2617-2629
Volume 62, Number 11, June 2022
- Fiorella Ruggiu
, Caitlin C. Bannan
, Andrea N. Bootsma
:
Early Career Perspectives from Large Pharma, Software, and Start-up Companies. 2631-2638 - Maciej Spiegel
:
Current Trends in Computational Quantum Chemistry Studies on Antioxidant Radical Scavenging Activity. 2639-2658 - Yuhong Wang
, Samuel G. Michael, Shyh-Ming Yang, Ruili Huang, Kennie Cruz-Gutierrez, Yaqing Zhang, Jinghua Zhao, Menghang Xia
, Paul Shinn, Hongmao Sun
:
Retro Drug Design: From Target Properties to Molecular Structures. 2659-2669 - Jiuyang Zhao
, Jacqueline M. Cole
:
Reconstructing Chromatic-Dispersion Relations and Predicting Refractive Indices Using Text Mining and Machine Learning. 2670-2684 - Navneet Bung
, Sowmya Ramaswamy Krishnan
, Arijit Roy
:
An In Silico Explainable Multiparameter Optimization Approach for De Novo Drug Design against Proteins from the Central Nervous System. 2685-2695 - Chao Yang
, Yingkai Zhang
:
Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions. 2696-2712 - Yuyang Wang
, Rishikesh Magar, Chen Liang, Amir Barati Farimani
:
Improving Molecular Contrastive Learning via Faulty Negative Mitigation and Decomposed Fragment Contrast. 2713-2725 - Michael C. Hutter
:
Differential Multimolecule Fingerprint for Similarity Search─Making Use of Active and Inactive Compound Sets in Virtual Screening. 2726-2736 - Andrea Jacobs
, Dustin Williams, Katherine Hickey, Nathan Patrick, Antony J. Williams
, Stuart J. Chalk
, Leah McEwen
, Egon L. Willighagen
, Martin Walker
, Evan Bolton
, Gabriel Sinclair
, Adam Sanford
:
CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community. 2737-2743 - Xiang Cai, Wei Han
:
Development of a Hybrid-Resolution Force Field for Peptide Self-Assembly Simulations: Optimizing Peptide-Peptide and Peptide-Solvent Interactions. 2744-2760 - Sinan Kardas
, Mathieu Fossépré, Vincent Lemaur
, Antony E. Fernandes
, Karine Glinel
, Alain M. Jonas
, Mathieu Surin
:
Revealing the Organization of Catalytic Sequence-Defined Oligomers via Combined Molecular Dynamics Simulations and Network Analysis. 2761-2770 - Francesca Galvani
, Laura Scalvini
, Silvia Rivara
, Alessio Lodola
, Marco Mor
:
Mechanistic Modeling of Monoglyceride Lipase Covalent Modification Elucidates the Role of Leaving Group Expulsion and Discriminates Inhibitors with High and Low Potency. 2771-2787 - Chaofeng Lou, Hongbin Yang
, Jiye Wang
, Mengting Huang, Weihua Li
, Guixia Liu
, Philip W. Lee, Yun Tang
:
IDL-PPBopt: A Strategy for Prediction and Optimization of Human Plasma Protein Binding of Compounds via an Interpretable Deep Learning Method. 2788-2799 - Louis Bellmann
, Raphael Klein
, Matthias Rarey
:
Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces. 2800-2810 - Adrien Varet, Nicolas Prcovic, Cyril Terrioux
, Denis Hagebaum-Reignier
, Yannick Carissan
:
BenzAI: A Program to Design Benzenoids with Defined Properties Using Constraint Programming. 2811-2820 - Abdul Basit
, Ajeet Kumar Yadav
, Pradipta Bandyopadhyay
:
Calcium Ion Binding to the Mutants of Calmodulin: A Structure-Based Computational Predictive Model of Binding Affinity Using a Charge Scaling Approach in Molecular Dynamics Simulation. 2821-2834 - Xu Yan, Yingfeng Lu, Zhen Li
, Qing Wei, Xin Gao
, Sheng Wang
, Song Wu
, Shuguang Cui:
PointSite: A Point Cloud Segmentation Tool for Identification of Protein Ligand Binding Atoms. 2835-2845 - Hiraku Oshima
, Yuji Sugita
:
Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions. 2846-2856 - José X. Lima Neto
, Davi S. Vieira, Jones de Andrade
, Umberto Laino Fulco
:
Exploring the Spike-hACE 2 Residue-Residue Interaction in Human Coronaviruses SARS-CoV-2, SARS-CoV, and HCoV-NL63. 2857-2868 - Xiyu Chen
, Sigrid Leyendecker, Henry van den Bedem
:
Kinematic Vibrational Entropy Assessment and Analysis of SARS CoV-2 Main Protease. 2869-2879 - Lijuan Yan, Yongjun Liu
:
Mechanistic Insights into the Anaerobic Degradation of Globally Abundant Dihydroxypropanesulfonate Catalyzed by the DHPS-Sulfolyase (HpsG). 2880-2888 - Norio Yoshida
, Yutaka Maruyama
, Ayori Mitsutake
, Akiyoshi Kuroda, Ryo Fujiki, Kodai Kanemaru, Daisuke Okamoto, Alexander E. Kobryn, Sergey Gusarov
, Haruyuki Nakano
:
Computational Analysis of the SARS-CoV-2 RBD-ACE2-Binding Process Based on MD and the 3D-RISM Theory. 2889-2898
Volume 62, Number 12, June 2022
- Issue Editorial Masthead.
- Issue Publication Information.
- Lydia Siragusa
, Gabriele Menna, Fabrizio Buratta, Massimo Baroni, Jenny Desantis, Gabriele Cruciani
, Laura Goracci
:
CROMATIC: Cross-Relationship Map of Cavities from Coronaviruses. 2901-2908 - Genki Imam Prayogo
, Andrea Tirelli
, Keishu Utimula
, Kenta Hongo
, Ryo Maezono
, Kousuke Nakano
:
Shry: Application of Canonical Augmentation to the Atomic Substitution Problem. 2909-2915 - Hao Wang, Xiaolin Pan
, Yueqing Zhang, Xingyu Wang, Xudong Xiao, Changge Ji
:
MolHyb: A Web Server for Structure-Based Drug Design by Molecular Hybridization. 2916-2922 - Huaipan Jiang
, Jian Wang
, Weilin Cong
, Yihe Huang
, Morteza Ramezani
, Anup Sarma
, Nikolay V. Dokholyan
, Mehrdad Mahdavi
, Mahmut T. Kandemir
:
Predicting Protein-Ligand Docking Structure with Graph Neural Network. 2923-2932 - Joonyoung F. Joung
, Minhi Han
, Minseok Jeong
, Sungnam Park
:
Beyond Woodward-Fieser Rules: Design Principles of Property-Oriented Chromophores Based on Explainable Deep Learning Optical Spectroscopy. 2933-2942 - Myeonghun Lee, Kyoungmin Min
:
MGCVAE: Multi-Objective Inverse Design via Molecular Graph Conditional Variational Autoencoder. 2943-2950 - Vincenzo Laveglia, Andrea Giachetti
, Davide Sala
, Claudia Andreini, Antonio Rosato
:
Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network. 2951-2960 - Erik Otovic
, Marko Njirjak
, Daniela Kalafatovic
, Goran Mausa
:
Sequential Properties Representation Scheme for Recurrent Neural Network-Based Prediction of Therapeutic Peptides. 2961-2972 - Jiahui Yu, Jike Wang, Hong Zhao, Junbo Gao, Yu Kang
, Dong-Sheng Cao
, Zhe Wang
, Tingjun Hou
:
Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism. 2973-2986 - Denis N. Prada Gori
, Manuel A. Llanos
, Carolina L. Bellera
, Alan Talevi
, Lucas N. Alberca
:
iRaPCA and SOMoC: Development and Validation of Web Applications for New Approaches for the Clustering of Small Molecules. 2987-2998 - Kosala Amarasinghe, Leonardo De Maria
, Christian Tyrchan
, Leif A. Eriksson
, Jens Sadowski, Dusan Petrovic
:
Virtual Screening Expands the Non-Natural Amino Acid Palette for Peptide Optimization. 2999-3007 - Manuel A. Llanos
, Nicolas Enrique
, María L. Sbaraglini
, Federico M. Garofalo
, Alan Talevi
, Luciana Gavernet
, Pedro Martín:
Structure-Based Virtual Screening Identifies Novobiocin, Montelukast, and Cinnarizine as TRPV1 Modulators with Anticonvulsant Activity In Vivo. 3008-3022 - Maria Antonietta La Serra
, Pietro Vidossich, Isabella Acquistapace
, Anand K. Ganesan, Marco de Vivo
:
Alchemical Free Energy Calculations to Investigate Protein-Protein Interactions: the Case of the CDC42/PAK1 Complex. 3023-3033 - Pedro R. Magalhães, Pedro B. P. S. Reis
, Diogo Vila-Viçosa, Miguel Machuqueiro
, Bruno L. Victor
:
Optimization of an in Silico Protocol Using Probe Permeabilities to Identify Membrane Pan-Assay Interference Compounds. 3034-3042 - Salomé Rieder
, Benjamin Ries
, Kay Schaller
, Candide Champion
, Emília P. Barros
, Philippe H. Hünenberger
, Sereina Riniker
:
Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules. 3043-3056 - Minjie Kang, Zhicheng Zuo
, Zhixiang Yin
, Jianrong Gu:
Molecular Mechanism of D1135E-Induced Discriminated CRISPR-Cas9 PAM Recognition. 3057-3066 - Daniel Bustos
, Erix Wiliam Hernández-Rodríguez
, Horacio Poblete, Jans H. Alzate-Morales
, Cecilia Challier
, Cristhian Boetsch
, Ariela Vergara Jaque
, Paola Beassoni
:
Structural Insights into the Inhibition Site in the Phosphorylcholine Phosphatase Enzyme of Pseudomonas aeruginosa. 3067-3078 - Adan Gallardo, Brandon M. Bogart, Bercem Dutagaci
:
Protein-Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations. 3079-3089 - Xueying Wang, Shuguang Yuan
, H. C. Stephen Chan:
Translocation Mechanism of Allosteric Sodium Ions in β2-Adrenoceptor. 3090-3095 - Jeremy Morere, Cécilia Hognon
, Tom Miclot, Tao Jiang
, Elise Dumont
, Giampaolo Barone
, Antonio Monari
, Emmanuelle Bignon
:
How Fragile We Are: Influence of Stimulator of Interferon Genes (STING) Variants on Pathogen Recognition and Immune Response Efficiency. 3096-3106 - Aria Gheeraert, Laurent Vuillon, Laurent Chaloin, Olivier Moncorgé, Thibaut Very, Serge Perez
, Vincent Leroux, Isaure Chauvot de Beauchêne
, Dominique Mias-Lucquin, Marie-Dominique Devignes, Ivan Rivalta
, Bernard Maigret:
Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis. 3107-3122 - Yongjun Zang, Luyang Tai, Yuanyang Hu, Yu Wang, Hongbin Sun
, Xiaoan Wen
, Haoliang Yuan
, Liang Dai
:
Discovery of a Novel Macrocyclic ATP Citrate Lyase Inhibitor. 3123-3132
Volume 62, Number 13, July 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Giulia Palermo
:
Celebrating Women of Color in Computational Chemistry. 3133-3134 - Reagan J. Meredith
, Luke Sernau, Anthony S. Serianni
:
MA'AT: A Web-Based Application to Determine Rotamer Population Distributions in Solution from Nuclear Magnetic Resonance Spin-Coupling Constants. 3135-3141 - Michael Schauperl
, Rajiah Aldrin Denny
:
AI-Based Protein Structure Prediction in Drug Discovery: Impacts and Challenges. 3142-3156 - Sangwoo Park
, Chaok Seok
:
GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network. 3157-3168 - Alexis W. Mills, Joshua J. Goings
, David Beck, Chao Yang, Xiaosong Li
:
Exploring Potential Energy Surfaces Using Reinforcement Machine Learning. 3169-3179 - Seid Hamzic, Richard A. Lewis
, Sandrine Desrayaud, Cihan Soylu, Mike Fortunato
, Grégori Gerebtzoff, Raquel Rodríguez-Pérez
:
Predicting In Vivo Compound Brain Penetration Using Multi-task Graph Neural Networks. 3180-3190 - Yuwei Yang, Zhenxing Wu
, Xiaojun Yao
, Yu Kang
, Tingjun Hou
, Chang-Yu Hsieh, Huanxiang Liu
:
Exploring Low-Toxicity Chemical Space with Deep Learning for Molecular Generation. 3191-3199 - Manuel A. Llanos
, Clara Ventura, Pedro Martín, Nicolas Enrique
, Juan I. Felice
, Luciana Gavernet
, Verónica Milesi:
Novel Dimeric hHv1 Model and Structural Bioinformatic Analysis Reveal an ATP-Binding Site Resulting in a Channel Activating Effect. 3200-3212 - Lingyan Wang, Kun Xi, Lizhe Zhu
, Lin-Tai Da
:
DNA Deformation Exerted by Regulatory DNA-Binding Motifs in Human Alkyladenine DNA Glycosylase Promotes Base Flipping. 3213-3226 - Zenghui Lao
, Xuewei Dong, Xianshi Liu, Fangying Li, Yujie Chen, Yiming Tang
, Guanghong Wei
:
Insights into the Atomistic Mechanisms of Phosphorylation in Disrupting Liquid-Liquid Phase Separation and Aggregation of the FUS Low-Complexity Domain. 3227-3238 - Abdelazim M. A. Abdelgawwad
, Antonio Monari
, Iñaki Tuñón
, Antonio Francés-Monerris
:
Spatial and Temporal Resolution of the Oxygen-Independent Photoinduced DNA Interstrand Cross-Linking by a Nitroimidazole Derivative. 3239-3252 - Lane W. Votapka, Andrew M. Stokely
, Anupam Anand Ojha
, Rommie E. Amaro
:
SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. 3253-3262 - Raitis Bobrovs
, Emils Edgars Basens, Laura Drunka, Iveta Kanepe, Sofija Matisone, Karlis Kristofers Velins, Victor Andrianov, Gundars Leitis, Diana Zelencova-Gopejenko
, Dace Rasina
, Aigars Jirgensons
, Kristaps Jaudzems
:
Exploring Aspartic Protease Inhibitor Binding to Design Selective Antimalarials. 3263-3273
Volume 62, Number 14, July 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Robert P. Sheridan, J. Christopher Culberson, Elizabeth Joshi, Matthew Tudor
, Prabha Karnachi:
Prediction Accuracy of Production ADMET Models as a Function of Version: Activity Cliffs Rule. 3275-3280 - Cunxing Lu
, Xili Wan
, Xuhao Ma, Xinjie Guan, Aichun Zhu:
Deep-Learning-Based End-to-End Predictions of CO2 Capture in Metal-Organic Frameworks. 3281-3290 - Jie Zhang
, Hongming Chen
:
De Novo Molecule Design Using Molecular Generative Models Constrained by Ligand-Protein Interactions. 3291-3306 - Ramil I. Nugmanov
, Natalia Dyubankova
, Andrey Gedich
, Jörg Kurt Wegner
:
Bidirectional Graphormer for Reactivity Understanding: Neural Network Trained to Reaction Atom-to-Atom Mapping Task. 3307-3315 - Yue Zhang
, Cong Wang
, Mya Soukaseum
, Dionisios G. Vlachos
, Hui Fang
:
Unleashing the Power of Knowledge Extraction from Scientific Literature in Catalysis. 3316-3330 - Fei Zhu, Sijie Yang, Fanwang Meng
, Yuxiang Zheng, Xin Ku
, Cheng Luo
, Guang Hu
, Zhongjie Liang
:
Leveraging Protein Dynamics to Identify Functional Phosphorylation Sites using Deep Learning Models. 3331-3345 - Beibei Wang
, Shane Jackson
, Aiichiro Nakano
, Ken-ichi Nomura, Priya Vashishta
, Rajiv K. Kalia, Mark Stevens
:
Neural Network for Principle of Least Action. 3346-3351 - Atsushi Tokuhisa
, Yoshinobu Akinaga, Kei Terayama
, Yuji Okamoto
, Yasushi Okuno:
Single-Image Super-Resolution Improvement of X-ray Single-Particle Diffraction Images Using a Convolutional Neural Network. 3352-3364 - Jesús Lucia-Tamudo
, Gustavo Cárdenas, Nuria Anguita-Ortiz, Sergio Díaz-Tendero
, Juan J. Nogueira
:
Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches. 3365-3380 - Amit Kumar
, Harish Vashisth
:
Role of Mutations in Differential Recognition of Viral RNA Molecules by Peptides. 3381-3390 - Kristoffer T. Bæk
, Kasper P. Kepp
:
Assessment of AlphaFold2 for Human Proteins via Residue Solvent Exposure. 3391-3400 - Marko Hanzevacki
, Anna K. Croft
, Christof M. Jäger
:
Activation of Glycyl Radical Enzymes─Multiscale Modeling Insights into Catalysis and Radical Control in a Pyruvate Formate-Lyase-Activating Enzyme. 3401-3414 - Anita Rácz
, Levente M. Mihalovits
, Dávid Bajusz
, Károly Héberger
, Ramón Alain Miranda-Quintana
:
Molecular Dynamics Simulations and Diversity Selection by Extended Continuous Similarity Indices. 3415-3425 - Maximilian Meixner
, Martin Zachmann, Sebastian Metzler, Jonathan Scheerer
, Martin Zacharias, Iris Antes:
Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock. 3426-3441 - Takunori Yasuda, Rikuri Morita
, Yasuteru Shigeta
, Ryuhei Harada
:
Structural Validation by the G-Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins. 3442-3452 - Prabir Khatua, Madhulika Gupta
, Sanjoy Bandyopadhyay
:
Exploring Heterogeneous Dynamical Environment around an Ensemble of Aβ42 Peptide Monomer Conformations. 3453-3462 - Hatice Gokcan
, Jirair K. Bedoyan, Olexandr Isayev
:
Simulations of Pathogenic E1α Variants: Allostery and Impact on Pyruvate Dehydrogenase Complex-E1 Structure and Function. 3463-3475
Volume 62, Number 15, August 2022
- Robert P. Sheridan
:
Stability of Prediction in Production ADMET Models as a Function of Version: Why and When Predictions Change. 3477-3485 - Miguel García-Ortegón
, Gregor N. C. Simm
, Austin J. Tripp
, José Miguel Hernández-Lobato
, Andreas Bender
, Sergio Bacallado
:
DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design. 3486-3502 - Zhengkai Tu, Connor W. Coley
:
Permutation Invariant Graph-to-Sequence Model for Template-Free Retrosynthesis and Reaction Prediction. 3503-3513 - Abdulmohsen A. Alsaui, Yousef A. Alghofaili, Mohammed Alghadeer, Fahhad H. Alharbi
:
Resampling Techniques for Materials Informatics: Limitations in Crystal Point Groups Classification. 3514-3523 - Tagir Akhmetshin
, Arkadii I. Lin, Daniyar Mazitov
, Yuliana Zabolotna
, Evgenii Ziaikin
, Timur I. Madzhidov
, Alexandre Varnek
:
HyFactor: A Novel Open-Source, Graph-Based Architecture for Chemical Structure Generation. 3524-3534 - Natália Aniceto
, Vasco D. B. Bonifácio
, Rita C. Guedes
, Nuno Martinho
:
Exploring the Chemical Space of Urease Inhibitors to Extract Meaningful Trends and Drivers of Activity. 3535-3550 - Vincent Blay
, Tijana Radivojevic, Jonathan E. Allen
, Corey M. Hudson
, Héctor García Martín
:
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design. 3551-3564 - Uschi Dolfus
, Hans Briem, Matthias Rarey
:
Synthesis-Aware Generation of Structural Analogues. 3565-3576 - Gonzalo F. Mayol, Lucas A. Defelipe
, Juan Pablo Arcon
, Adrian Gustavo Turjanski
, Marcelo A. Marti
:
Solvent Sites Improve Docking Performance of Protein-Protein Complexes and Protein-Protein Interface-Targeted Drugs. 3577-3588 - Bregje W. Brinkmann
, Ankush Singhal, G. J. Agur Sevink, Lisette Neeft, Martina G. Vijver, Willie J. G. M. Peijnenburg:
Predicted Adsorption Affinity for Enteric Microbial Metabolites to Metal and Carbon Nanomaterials. 3589-3603 - Walter Fiedler, Fabian Freisleben, Jasmin Wellbrock, Karl N. Kirschner
:
Mebendazole's Conformational Space and Its Predicted Binding to Human Heat-Shock Protein 90. 3604-3617 - Pedro A. Valiente
, Satra Nim, Jinah Lee
, Seungtaek Kim, Philip M. Kim
:
Targeting the Receptor-Binding Motif of SARS-CoV-2 with D-Peptides Mimicking the ACE2 Binding Helix: Lessons for Inhibiting Omicron and Future Variants of Concern. 3618-3626 - Shih-Hsien Liu
, Zhousheng Xiao, Sambit K. Mishra
, Julie C. Mitchell
, Jeremy C. Smith
, L. Darryl Quarles, Loukas Petridis:
Identification of Small-Molecule Inhibitors of Fibroblast Growth Factor 23 Signaling via In Silico Hot Spot Prediction and Molecular Docking to α-Klotho. 3627-3637 - Rui P. P. Neves
, Pedro Alexandrino Fernandes
, Maria João Ramos
:
Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by α-Amylase Explored with QM/MM Molecular Dynamics. 3638-3650 - Tao Jiang, Zhenhao Liu, Wenlang Liu, Jiawen Chen, Zheng Zheng
, Mojie Duan
:
The Conformational Transition Pathways and Hidden Intermediates in DFG-Flip Process of c-Met Kinase Revealed by Metadynamics Simulations. 3651-3663 - Dan Teng
, Yang Zhou
, Yun Tang
, Guixia Liu
, Yaoquan Tu
:
Mechanistic Studies on the Stereoselectivity of FFAR1 Modulators. 3664-3675 - Jingjing Zheng
, Yurong Qian, Jie He, Zerui Kang, Lei Deng:
Graph Neural Network with Self-Supervised Learning for Noncoding RNA-Drug Resistance Association Prediction. 3676-3684
Volume 62, Number 16, August 2022
- Filipe Menezes
, Grzegorz M. Popowicz
:
ULYSSES: An Efficient and Easy to Use Semiempirical Library for C++. 3685-3694 - Chaoshu Duan, Xuyang Liu
, Wensheng Cai
, Xueguang Shao
:
Spectral Encoder to Extract the Features of Near-Infrared Spectra for Multivariate Calibration. 3695-3703 - Alexandra Wahab
, Lara Pfuderer, Eno Paenurk
, Renana Gershoni-Poranne
:
The COMPAS Project: A Computational Database of Polycyclic Aromatic Systems. Phase 1: cata-Condensed Polybenzenoid Hydrocarbons. 3704-3713 - Florian Spenke, Bernd Hartke
:
Graph-based Automated Macro-Molecule Assembly. 3714-3723 - Ethan King, Richard Overstreet, Julia Nguyen, Danielle Ciesielski
:
Augmentation of MS/MS Libraries with Spectral Interpolation for Improved Identification. 3724-3733 - Andrés Sánchez-Ruiz
, Gonzalo Colmenarejo
:
Systematic Analysis and Prediction of the Target Space of Bioactive Food Compounds: Filling the Chemobiological Gaps. 3734-3751 - Kunal Kumar Jha
, Barbara Gruza
, Aleksandra Sypko, Prashant Kumar
, Michal Chodkiewicz
, Paulina Maria Dominiak
:
Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB. 3752-3765 - Paulina Maria Rybicka
, Marta Kulik
, Michal Chodkiewicz
, Paulina Maria Dominiak
:
Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Impact of Surrounding Atoms on Electron Density from Cluster Analysis. 3766-3783 - Stefania Monteleone, Dmitri G. Fedorov
, Andrea Townsend-Nicholson
, Michelle Southey, Michael J. Bodkin, Alexander Heifetz
:
Hotspot Identification and Drug Design of Protein-Protein Interaction Modulators Using the Fragment Molecular Orbital Method. 3784-3799 - Nisha Amarnath Jonniya
, Parimal Kar
:
Functional Loop Dynamics and Characterization of the Inactive State of the NS2B-NS3 Dengue Protease due to Allosteric Inhibitor Binding. 3800-3813 - Mehdi Sahihi
, Jordi Faraudo
:
Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface. 3814-3824 - Asuka A. Orr
, Suliman Sharif, Junmei Wang
, Alexander D. MacKerell Jr.
:
Preserving the Integrity of Empirical Force Fields. 3825-3831 - Dusan Petrovic
, James S. Scott
, Michael S. Bodnarchuk
, Olivier Lorthioir, Scott Boyd, George M. Hughes
, Jordan Lane
, Allan Wu, David Hargreaves, James Robinson
, Jens Sadowski:
Virtual Screening in the Cloud Identifies Potent and Selective ROS1 Kinase Inhibitors. 3832-3843 - Zsolt Fazekas
, Dóra K. Menyhárd
, András Perczel
:
Omicron Binding Mode: Contact Analysis and Dynamics of the Omicron Receptor-Binding Domain in Complex with ACE2. 3844-3853 - David E. Graff, Matteo Aldeghi
, Joseph A. Morrone
, Kirk E. Jordan, Edward O. Pyzer-Knapp
, Connor W. Coley
:
Self-Focusing Virtual Screening with Active Design Space Pruning. 3854-3862 - Han Liu
, Haohao Fu
, Christophe Chipot
, Xueguang Shao
, Wensheng Cai
:
Accurate Description of Solvent-Exposed Salt Bridges with a Non-polarizable Force Field Incorporating Solvent Effects. 3863-3873 - Nicole Balasco, Antonella Paladino
, Giuseppe Graziano, Marco D'Abramo
, Luigi Vitagliano:
Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs. 3874-3884 - Viet Hoang Man
, Xibing He
, Junmei Wang
:
Stable Cavitation Interferes with Aβ16-22 Oligomerization. 3885-3895 - Mitja Ogrizek, Matej Janezic
, Katja Valjavec, Andrej Perdih
:
Catalytic Mechanism of ATP Hydrolysis in the ATPase Domain of Human DNA Topoisomerase IIα. 3896-3909 - Rino Ragno
, Anna Minarini, Eleonora Proia, Lorenzo Antonini, Andrea Milelli
, Vincenzo Tumiatti, Marco Fiore, Pasquale Fino, Lavinia Rutigliano
, Rossella Fioravanti, Tomoaki Tahara, Elena Pacella
, Antonio Greco, Gianluca Canettieri, Maria Luisa Di Paolo
, Enzo Agostinelli
:
Bovine Serum Amine Oxidase and Polyamine Analogues: Chemical Synthesis and Biological Evaluation Integrated with Molecular Docking and 3-D QSAR Studies. 3910-3927 - Carlos Santiago
, Bernabé Ortega-Tenezaca
, Iratxe Barbolla
, Brenda Fundora-Ortiz, Sonia Arrasate
, María Auxiliadora Dea-Ayuela
, Humberto González Díaz
, Nuria Sotomayor
, Esther Lete
:
Prediction of Antileishmanial Compounds: General Model, Preparation, and Evaluation of 2-Acylpyrrole Derivatives. 3928-3940
Volume 62, Number 17, September 2022
- Guo-Wei Wei
, Feng Zhu
, Kenneth M. Merz Jr.
:
Editorial on Machine Learning. 3941 - Thomas Fox
, Michael Bieler, Peter Haebel, Rodrigo Ochoa, Stefan Peters, Alexander Weber
:
BILN: A Human-Readable Line Notation for Complex Peptides. 3942-3947 - Gabriel A. Pinheiro
, Juarez L. F. Da Silva
, Marcos G. Quiles
:
SMICLR: Contrastive Learning on Multiple Molecular Representations for Semisupervised and Unsupervised Representation Learning. 3948-3960 - Xiang Liu
, Huitao Feng, Jie Wu, Kelin Xia
:
Hom-Complex-Based Machine Learning (HCML) for the Prediction of Protein-Protein Binding Affinity Changes upon Mutation. 3961-3969 - Hugo Bellamy
, Abbi Abdel-Rehim, Oghenejokpeme I. Orhobor, Ross D. King:
Batched Bayesian Optimization for Drug Design in Noisy Environments. 3970-3981 - Katsuhisa Morita, Tadahaya Mizuno
, Hiroyuki Kusuhara:
Investigation of a Data Split Strategy Involving the Time Axis in Adverse Event Prediction Using Machine Learning. 3982-3992 - Qinghua Wang, Zhe Wang
, Sheng Tian
, Lingling Wang, Rongfan Tang, Yang Yu, Jingxuan Ge, Tingjun Hou
, Haiping Hao, Huiyong Sun
:
Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning. 3993-4007 - Wenjian Ma
, Shugang Zhang
, Zhen Li
, Mingjian Jiang
, Shuang Wang, Weigang Lu, Xiangpeng Bi, Huasen Jiang, Henggui Zhang, Zhiqiang Wei:
Enhancing Protein Function Prediction Performance by Utilizing AlphaFold-Predicted Protein Structures. 4008-4017 - Gulnara Shavalieva
, Stavros Papadokonstantakis
, Gregory Peters
:
Prior Knowledge for Predictive Modeling: The Case of Acute Aquatic Toxicity. 4018-4031 - Ryuichiro Ishitani
, Toshiki Kataoka, Kentaro Rikimaru
:
Molecular Design Method Using a Reversible Tree Representation of Chemical Compounds and Deep Reinforcement Learning. 4032-4048 - Parker Ladd Bremer, Arpana Vaniya, Tobias Kind
, Shunyang Wang, Oliver Fiehn
:
How Well Can We Predict Mass Spectra from Structures? Benchmarking Competitive Fragmentation Modeling for Metabolite Identification on Untrained Tandem Mass Spectra. 4049-4056 - Hiroaki Iwata
, Tatsuru Matsuo, Hideaki Mamada
, Takahisa Motomura, Mayumi Matsushita, Takeshi Fujiwara, Kazuya Maeda, Koichi Handa
:
Predicting Total Drug Clearance and Volumes of Distribution Using the Machine Learning-Mediated Multimodal Method through the Imputation of Various Nonclinical Data. 4057-4065 - Justin Legleiter
, Ravindra Thakkar, Astrid Velásquez-Silva
, Ingrid Miranda-Carvajal, Susan Whitaker, John Tomich
, Jeffrey Comer
:
Design of Peptides that Fold and Self-Assemble on Graphite. 4066-4082 - Alberto M. dos Santos, Amanda Ruslana Santana Oliveira, Clauber Henrique Costa
, Peter W. Kenny
, Carlos Alberto Montanari
, Jaldyr de Jesus G. Varela
, Jerônimo Lameira
:
Assessment of Reversibility for Covalent Cysteine Protease Inhibitors Using Quantum Mechanics/Molecular Mechanics Free Energy Surfaces. 4083-4094 - Ebru Akkus
, Omer Tayfuroglu
, Muslum Yildiz, Abdulkadir Kocak
:
Accurate Binding Free Energy Method from End-State MD Simulations. 4095-4106 - Emilian Tuca
, Gino Dilabio
, Alberto Otero-de-la-Roza
:
Minimal Basis Set Hartree-Fock Corrected with Atom-Centered Potentials for Molecular Crystal Modeling and Crystal Structure Prediction. 4107-4121 - Yongna Yuan
, Haoqiu Yan, Zeyang Cui
, Zhenyu Liu, Wei Su
, Ruisheng Zhang:
Quantum Chemical Calculations with Machine Learning for Multipolar Electrostatics Prediction in RNA: An Application to Pentose. 4122-4133 - Elisabeth Kallert
, Tim R. Fischer, Simon Schneider, Maike Grimm, Mark Helm
, Christian Kersten
:
Protein-Based Virtual Screening Tools Applied for RNA-Ligand Docking Identify New Binders of the preQ1-Riboswitch. 4134-4148 - Evan Gildernew, Sungwoo Yang
:
Finite Element Modeling of Atmospheric Water Extraction by Way of Highly Porous Adsorbents: A Roadmap for Solver Construction with Model Factor Sensitivity Screening. 4149-4161 - Duván González, Luis Macaya, Carlos Castillo-Orellana
, Toon Verstraelen
, Stefan Vogt-Geisse, Esteban Vöhringer-Martinez
:
Nonbonded Force Field Parameters from Minimal Basis Iterative Stockholder Partitioning of the Molecular Electron Density Improve CB7 Host-Guest Affinity Predictions. 4162-4174 - Iris N. Smith, Jennifer E. Dawson, James Krieger, Stetson Thacker, Ivet Bahar
, Charis Eng
:
Structural and Dynamic Effects of PTEN C-Terminal Tail Phosphorylation. 4175-4190 - K. Michael Salerno
, Janna Domenico
, Nam Q. Le, Christopher D. Stiles
, Ilia A. Solov'yov
, Carlos F. Martino:
Long-Time Oxygen Localization in Electron Transfer Flavoprotein. 4191-4199 - Lukas Schulig
, Norman Geist
, Mihaela Delcea
, Andreas Link
, Martin Kulke
:
Fundamental Redesign of the TIGER2hs Kernel to Address Severe Parameter Sensitivity. 4200-4209 - Bin Sun
, Peter M. Kekenes-Huskey
:
Calmodulin's Interdomain Linker Is Optimized for Dynamics Signal Transmission and Calcium Binding. 4210-4221 - Hao Zhang, Duan Ni, Jigang Fan, Minyu Li, Jian Zhang
, Chen Hua, Ruth Nussinov
, Shaoyong Lu
:
Markov State Models and Molecular Dynamics Simulations Reveal the Conformational Transition of the Intrinsically Disordered Hypervariable Region of K-Ras4B to the Ordered Conformation. 4222-4231 - Osita Sunday Nnyigide, Tochukwu Olunna Nnyigide, Sun-Gu Lee
, Kyu Hyun
:
Protein Repair and Analysis Server: A Web Server to Repair PDB Structures, Add Missing Heavy Atoms and Hydrogen Atoms, and Assign Secondary Structures by Amide Interactions. 4232-4246 - Sayyed Jalil Mahdizadeh
, Emil Pålsson, Antonio Carlesso, Eric Chevet
, Leif A. Eriksson
:
QM/MM Well-Tempered Metadynamics Study of the Mechanism of XBP1 mRNA Cleavage by Inositol Requiring Enzyme 1α RNase. 4247-4260 - Emmanuelle Bignon
, Antonio Monari
:
Modeling the Enzymatic Mechanism of the SARS-CoV-2 RNA-Dependent RNA Polymerase by DFT/MM-MD: An Unusual Active Site Leading to High Replication Rates. 4261-4269 - Shahid Iqbal, Fang Ge, Fuyi Li
, Tatsuya Akutsu, Yuanting Zheng, Robin B. Gasser
, Dong-Jun Yu
, Geoffrey I. Webb
, Jiangning Song
:
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations. 4270-4282 - Guan-Yu Zhu, Yan Liu, Peng-Hao Wang, Xibei Yang, Dong-Jun Yu
:
Learning Protein Embedding to Improve Protein Fold Recognition Using Deep Metric Learning. 4283-4291 - Giulia Palermo
:
Celebrating the Next Generation of Women in Computational Chemistry to Increase Diversity, Equity, Inclusion, and Respect. 4292-4293
Volume 62, Number 18, September 2022
- Jannis Born
, Yoel Shoshan, Tien Huynh, Wendy D. Cornell, Eric J. Martin
, Matteo Manica
:
On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction. 4295-4299 - Alexandre V. Fassio
, Laura Shub
, Luca Ponzoni
, Jessica McKinley
, Matthew J. O'Meara
, Rafaela Salgado Ferreira, Michael J. Keiser
, Raquel Cardoso de Melo Minardi
:
Prioritizing Virtual Screening with Interpretable Interaction Fingerprints. 4300-4318 - Wan Nie
, Deguang Liu
, Shuaicheng Li, Haizhu Yu, Yao Fu
:
Nucleophilicity Prediction Using Graph Neural Networks. 4319-4328 - Md. Masud Rana
, Duc Duy Nguyen
:
EISA-Score: Element Interactive Surface Area Score for Protein-Ligand Binding Affinity Prediction. 4329-4341 - Madeleine D. Breshears
, Rajiv Giridharagopal
, Justin Pothoof
, David S. Ginger
:
A Robust Neural Network for Extracting Dynamics from Electrostatic Force Microscopy Data. 4342-4350 - Thijs Beuming
, Helena Martín
, Anna M. Díaz-Rovira
, Lucía Díaz
, Victor Guallar, Soumya S. Ray:
Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures. 4351-4360 - Xue Zong, Dionisios G. Vlachos
:
Exploring Structure-Sensitive Relations for Small Species Adsorption Using Machine Learning. 4361-4368 - Xiaoyang Qu, Lina Dong, Jinyan Zhang, Yubing Si
, Binju Wang
:
Systematic Improvement of the Performance of Machine Learning Scoring Functions by Incorporating Features of Protein-Bound Water Molecules. 4369-4379 - Qingyu Li
, Xiaochang Zhang, Lianlian Wu, Xiaochen Bo, Song He, Shengqi Wang:
PLA-MoRe: A Protein-Ligand Binding Affinity Prediction Model via Comprehensive Molecular Representations. 4380-4390 - Daniel J. Woodward
, Anthony R. Bradley, Willem P. van Hoorn
:
Coverage Score: A Model Agnostic Method to Efficiently Explore Chemical Space. 4391-4402 - Shunyang Wang, Tobias Kind
, Parker Ladd Bremer, Dean J. Tantillo
, Oliver Fiehn
:
Beyond the Ground State: Predicting Electron Ionization Mass Spectra Using Excited-State Molecular Dynamics. 4403-4410 - Mohamed Korany, Ida Ritacco
, Eslam Dabbish
, Emilia Sicilia
, Tamer Shoeib
:
Analysis of the Fragmentation Pathways for the Collision-Induced Dissociation of Protonated Cyclophosphamide: A Mass Spectrometry and Quantum Mechanical Study. 4411-4419 - Liming Zhao, Mengchen Pu
, Huting Wang, Xiangyu Ma, Yingsheng J. Zhang
:
Modified Electrostatic Complementary Score Function and Its Application Boundary Exploration in Drug Design. 4420-4426 - Masato Sumita
, Kei Terayama
, Ryo Tamura
, Koji Tsuda
:
QCforever: A Quantum Chemistry Wrapper for Everyone to Use in Black-Box Optimization. 4427-4434 - António M. Baptista
, Lucie da Rocha
, Sara R. R. Campos
:
FixBox: A General Algorithm to Fix Molecular Systems in Periodic Boxes. 4435-4447 - Yuan Hu
, Ingo Muegge
:
In Silico Positional Analogue Scanning with Amber GPU-TI. 4448-4459 - Kosuke Kawama, Yusaku Fukushima, Mitsunori Ikeguchi
, Masateru Ohta
, Takashi Yoshidome
:
gr Predictor: A Deep Learning Model for Predicting the Hydration Structures around Proteins. 4460-4473 - Azamat Rizuan
, Nina Jovic, Tien M. Phan
, Young C. Kim, Jeetain Mittal
:
Developing Bonded Potentials for a Coarse-Grained Model of Intrinsically Disordered Proteins. 4474-4485 - Rachel T. Payne, Silvia Crivelli, Masakatsu Watanabe
:
All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System. 4486-4499 - Taeho Kim, Kewon Kim, Inyoung Park, Sungwoo Hong
, Hwangseo Park
:
Two-Track Virtual Screening Approach to Identify the Dual Inhibitors of Wild Type and C481S Mutant of Bruton's Tyrosine Kinase. 4500-4511 - Liping Zhou, Tingting Liu, Mengxia Mo, Yulong Shi, Leyun Wu, Yishui Li, Qiuping Qin
, Weiliang Zhu
, Chengkun Wu, Likun Gong, Zhijian Xu
:
Exploring the Binding Affinity and Mechanism between ACE2 and the Trimers of Delta and Omicron Spike Proteins by Molecular Dynamics Simulation and Bioassay. 4512-4522 - Yumeng Zhang
, Xiaorong Liu
, Jianhan Chen
:
Toward Accurate Coarse-Grained Simulations of Disordered Proteins and Their Dynamic Interactions. 4523-4536 - Yuliana Zabolotna
, Fanny Bonachéra, Dragos Horvath
, Arkadii I. Lin, Gilles Marcou
, Olga Klimchuk, Alexandre Varnek
:
Chemspace Atlas: Multiscale Chemography of Ultralarge Libraries for Drug Discovery. 4537-4548 - Masatake Sugita
, Takuya Fujie
, Keisuke Yanagisawa
, Masahito Ohue
, Yutaka Akiyama
:
Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations. 4549-4560 - José Ramón López-Blanco
, Yves Dehouck
, Ugo Bastolla
, Pablo Chacón
:
Local Normal Mode Analysis for Fast Loop Conformational Sampling. 4561-4568
Volume 62, Number 19, October 2022
- Thanh T. Lai
, David M. Kuntz, Angela K. Wilson
:
Molecular Screening and Toxicity Estimation of 260, 000 Perfluoroalkyl and Polyfluoroalkyl Substances (PFASs) through Machine Learning. 4569-4578 - Zhipeng Wu
, Xiang Cai, Chengyun Zhang, Haoran Qiao, Yejian Wu, Yun Zhang, Xinqiao Wang
, Haiying Xie, Feng Luo, Hongliang Duan
:
Self-Supervised Molecular Pretraining Strategy for Low-Resource Reaction Prediction Scenarios. 4579-4590 - Simon Bray
, Victor Tänzel
, Steffen Wolf
:
Ligand Unbinding Pathway and Mechanism Analysis Assisted by Machine Learning and Graph Methods. 4591-4604 - Billy J. Williams-Noonan
, Melissa N. Speer, Tu C. Le
, Maiada M. Sadek
, Philip E. Thompson
, Raymond S. Norton
, Elizabeth Yuriev
, Nicholas Barlow
, David K. Chalmers
, Irene Yarovsky
:
Membrane Permeating Macrocycles: Design Guidelines from Machine Learning. 4605-4619 - María Isabel Sánchez-Rodríguez
, Elena Sánchez-López
, Alberto Marinas
, José María Caridad, Francisco José Urbano:
Redundancy Analysis to Reduce the High-Dimensional Near-Infrared Spectral Information to Improve the Authentication of Olive Oil. 4620-4628 - Yuchi Qiu
, Guo-Wei Wei
:
CLADE 2.0: Evolution-Driven Cluster Learning-Assisted Directed Evolution. 4629-4641 - Agamemnon Krasoulis
, Nick Antonopoulos
, Vassilis Pitsikalis, Stavros Theodorakis:
DENVIS: Scalable and High-Throughput Virtual Screening Using Graph Neural Networks with Atomic and Surface Protein Pocket Features. 4642-4659 - Matteo Aldeghi
, David E. Graff, Nathan C. Frey
, Joseph A. Morrone
, Edward O. Pyzer-Knapp
, Kirk E. Jordan, Connor W. Coley
:
Roughness of Molecular Property Landscapes and Its Impact on Modellability. 4660-4671 - Bo Yang
, David Hawley, Jianhua Yao, Camille May, Jose E. Mendez-Arroyo, Daniel H. Ess
:
Demonstration of High-Throughput Building Block and Composition Analysis of Metal-Organic Frameworks. 4672-4679 - Uschi Dolfus
, Hans Briem, Matthias Rarey
:
Visualizing Generic Reaction Patterns. 4680-4689 - Denys E. S. Santos
, Kaline Coutinho
, Thereza A. Soares
:
Surface Assessment via Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape. 4690-4701 - Alex S. Moraes
, Gabriel A. Pinheiro
, Tuanan C. Lourenço
, Mauro C. Lopes
, Marcos G. Quiles
, Luis Gustavo Dias
, Juarez L. F. Da Silva
:
Screening of the Role of the Chemical Structure in the Electrochemical Stability Window of Ionic Liquids: DFT Calculations Combined with Data Mining. 4702-4712 - Julián A. Delgado, Vered Wineman-Fisher
, Sagar Pandit
, Sameer Varma
:
Inclusion of High-Field Target Data in AMOEBA's Calibration Improves Predictions of Protein-Ion Interactions. 4713-4726 - Surajit Nandi
, Jonas Busk, Peter Bjørn Jørgensen, Tejs Vegge
, Arghya Bhowmik
:
Cheap Turns Superior: A Linear Regression-Based Correction Method to Reaction Energy from the DFT. 4727-4735 - Tianyi Ding, Dmitry Karlov
, Almudena Pino-Ángeles
, Irina G. Tikhonova
:
Intermolecular Interactions in G Protein-Coupled Receptor Allosteric Sites at the Membrane Interface from Molecular Dynamics Simulations and Quantum Chemical Calculations. 4736-4747 - Bruno Giovanni Galuzzi, Antonio Mirarchi, Edoardo Luca Viganò
, Luca De Gioia, Chiara Damiani, Federica Arrigoni
:
Machine Learning for Efficient Prediction of Protein Redox Potential: The Flavoproteins Case. 4748-4759 - Melisa E. Gantner
, Denis N. Prada Gori
, Manuel A. Llanos
, Alan Talevi
, Andrea Angeli
, Daniela Vullo, Claudiu T. Supuran
, Luciana Gavernet
:
Identification of New Carbonic Anhydrase VII Inhibitors by Structure-Based Virtual Screening. 4760-4770 - Anastasia Croitoru
, Alexey Aleksandrov
:
Parametrization of Force Field Bonded Terms under Structural Inconsistency. 4771-4782 - Jirí Vymetal
, Jirí Vondrásek
:
Iterative Landmark-Based Umbrella Sampling (ILBUS) Protocol for Sampling of Conformational Space of Biomolecules. 4783-4798 - Alan Fernando Rodríguez Serrano
, I-Ming Hsing
:
Prediction of Aptamer-Small-Molecule Interactions Using Metastable States from Multiple Independent Molecular Dynamics Simulations. 4799-4809 - Santhosh Sankar
, Naren Chandran Sakthivel
, Nagasuma Chandra
:
Fast Local Alignment of Protein Pockets (FLAPP): A System-Compiled Program for Large-Scale Binding Site Alignment. 4810-4819 - Quang-Hien Kha, Quang-Thai Ho, Nguyen-Quoc-Khanh Le
:
Identifying SNARE Proteins Using an Alignment-Free Method Based on Multiscan Convolutional Neural Network and PSSM Profiles. 4820-4826
Volume 62, Number 20, October 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Saba Iftkhar
, Alex G. C. de Sá, João P. L. Velloso, Raghad Al-Jarf, Douglas E. V. Pires
, David B. Ascher
:
cardioToxCSM: A Web Server for Predicting Cardiotoxicity of Small Molecules. 4827-4836 - Megumi Iwayama
, Stephen Wu
, Chang Liu
, Ryo Yoshida
:
Functional Output Regression for Machine Learning in Materials Science. 4837-4851 - Hisham Abdel-Aty, Ian R. Gould
:
Large-Scale Distributed Training of Transformers for Chemical Fingerprinting. 4852-4862 - Sara Romeo Atance
, Juan Viguera Diez
, Ola Engkvist
, Simon Olsson
, Rocío Mercado
:
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models. 4863-4872 - Chuan Li, Chenghui Wang, Ming Sun, Yan Zeng, Yuan Yuan, Qiaolin Gou, Guangchuan Wang, Yanzhi Guo, Xuemei Pu
:
Correlated RNN Framework to Quickly Generate Molecules with Desired Properties for Energetic Materials in the Low Data Regime. 4873-4887 - Gabriel Sinclair
, Inthirany Thillainadarajah, Brian Meyer, Vicente Samano, Sakuntala Sivasupramaniam, Linda Adams, Egon L. Willighagen
, Ann M. Richard
, Martin Walker
, Antony J. Williams
:
Wikipedia on the CompTox Chemicals Dashboard: Connecting Resources to Enrich Public Chemical Data. 4888-4905 - Matthew S. Johnson
, Xiaorui Dong
, Alon Grinberg Dana
, Yunsie Chung
, David Farina
, Ryan J. Gillis
, Mengjie Liu
, Nathan W. Yee, Katrin Blondal
, Emily J. Mazeau
, Colin A. Grambow, A. Mark Payne
, Kevin A. Spiekermann
, Hao-Wei Pang
, C. Franklin Goldsmith
, Richard H. West
, William H. Green Jr.
:
RMG Database for Chemical Property Prediction. 4906-4915 - Angela Parise, Giada Ciardullo, Mario Prejanò
, Aurélien de la Lande
, Tiziana Marino
:
On the Recognition of Natural Substrate CTP and Endogenous Inhibitor ddhCTP of SARS-CoV-2 RNA-Dependent RNA Polymerase: A Molecular Dynamics Study. 4916-4927 - Qingqing Jia, Yifan Ni, Ziteng Liu, Xu Gu, Ziyi Cui, Mengting Fan, Qiang Zhu
, Yi Wang
, Jing Ma
:
Fast Prediction of Lipophilicity of Organofluorine Molecules: Deep Learning-Derived Polarity Characters and Experimental Tests. 4928-4936 - Amanda E. Wakefield
, Dávid Bajusz
, Dima Kozakov
, György M. Keserü
, Sandor Vajda
:
Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors. 4937-4954 - Rudramani Pokhrel
, Rojesh Shakya, Prabin Baral, Prem Chapagain
:
Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus. 4955-4962 - Lukács J. Németh, Tamás A. Martinek
, Balázs Jójárt
:
Tilted State Population of Antimicrobial Peptide PGLa Is Coupled to the Transmembrane Potential. 4963-4969 - Xiaochen Cui, Hao Liu
, Hai-Feng Chen
:
Polarizable Force Field of Intrinsically Disordered Proteins with CMAP and Reweighting Optimization. 4970-4982 - Haiyi Zhang
, Xiyao Zhang, Guanhong Huang, Feifei Li, Fengmei Wu, Chunfang Xie, Daling Liu, Dongsheng Yao:
Screening ssDNA Aptamers Against Human Vascular Endothelial Factor 165 via Semirational Design. 4983-4991 - Isabell Louise Grothaus
, Giovanni Bussi
, Lucio Colombi Ciacchi
:
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans. 4992-5008 - Xin Yang, Guifeng Lin
, Anjie Xia
, Jingming Liu, Shiyu Zhang, Pei Zhou, Yiwei Wang, Jiahao Zhang, Yangli Zhou, Pei Chen, Yifei Wang
, Tao Zheng, Linli Li, Sheng-Yong Yang
:
Discovery of Small Molecule Agonist of Gonadotropin-Releasing Hormone Receptor (GnRH1R). 5009-5022 - Carla F. Sousa
, Mohamed A. M. Kamal, Robert Richter, Kalanika Elamaldeniya, Rolf W. Hartmann, Martin Empting
, Claus-Michael Lehr
, Olga V. Kalinina:
Modeling the Effect of Hydrophobicity on the Passive Permeation of Solutes across a Bacterial Model Membrane. 5023-5033
Volume 62, Number 21, November 2022
- Guo-Wei Wei
, Thereza A. Soares
, Habibah A. Wahab
, Feng Zhu
:
Computational Chemistry in Asia. 5035-5037 - Pengcheng Xu, Dongping Chang, Tian Lu, Long Li, Minjie Li
, Wencong Lu
:
Search for ABO3 Type Ferroelectric Perovskites with Targeted Multi-Properties by Machine Learning Strategies. 5038-5049 - Thanh-Hoang Nguyen-Vo
, Quang H. Trinh
, Loc Nguyen
, Trang T. T. Do
, Matthew Chin Heng Chua
, Binh P. Nguyen
:
Predicting Antimalarial Activity in Natural Products Using Pretrained Bidirectional Encoder Representations from Transformers. 5050-5058 - Thanh-Hoang Nguyen-Vo
, Quang H. Trinh
, Loc Nguyen
, Phuong-Uyen Nguyen-Hoang
, Thien-Ngan Nguyen
, Dung T. Nguyen
, Binh P. Nguyen
, Ly Le
:
iCYP-MFE: Identifying Human Cytochrome P450 Inhibitors Using Multitask Learning and Molecular Fingerprint-Embedded Encoding. 5059-5068 - Rishal Aggarwal, Akash Gupta
, Vineeth R. Chelur, C. V. Jawahar, U. Deva Priyakumar
:
DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks. 5069-5079 - Loc Nguyen
, Thanh-Hoang Nguyen-Vo
, Quang H. Trinh
, Bach Hoai Nguyen, Phuong-Uyen Nguyen-Hoang
, Ly Le
, Binh P. Nguyen
:
iANP-EC: Identifying Anticancer Natural Products Using Ensemble Learning Incorporated with Evolutionary Computation. 5080-5089 - Wenze Li, Donghan Wang, Zirui Yang, Huijie Zhang, Li Hong Hu
, Guanhua Chen
:
DeepNCI: DFT Noncovalent Interaction Correction with Transferable Multimodal Three-Dimensional Convolutional Neural Networks. 5090-5099 - Sowmya Ramaswamy Krishnan
, Navneet Bung
, Sarveswara Rao Vangala, Rajgopal Srinivasan, Gopalakrishnan Bulusu
, Arijit Roy
:
De Novo Structure-Based Drug Design Using Deep Learning. 5100-5109 - Mengrong Li
, Miaomiao Li
, Jingjing Guo
:
Molecular Mechanism of Ca2+ in the Allosteric Regulation of Human Parathyroid Hormone Receptor-1. 5110-5119 - Fuhui Zhang, Xin Chen, Jianfang Chen, Yanjiani Xu, Shiqi Li, Yanzhi Guo, Xuemei Pu
:
Probing Allosteric Regulation Mechanism of W7.35 on Agonist-Induced Activity for μOR by Mutation Simulation. 5120-5135 - Yang Wang
:
Extension and Quantification of the Fries Rule and Its Connection to Aromaticity: Large-Scale Validation by Wave-Function-Based Resonance Analysis. 5136-5148 - Donghui Huo, Shiyu Wang
, Yue Kong
, Zijian Qin, Aixia Yan
:
Discovery of Novel Epidermal Growth Factor Receptor (EGFR) Inhibitors Using Computational Approaches. 5149-5164 - Shaoli Cui
, Weijia Zhang
, Xueguang Shao
, Wensheng Cai
:
Hyperactive Antifreeze Proteins Promote Ice Growth before Binding to It. 5165-5174 - Jianfang Chen, Jiangting Liu, Yuan Yuan, Xin Chen, Fuhui Zhang, Xuemei Pu
:
Molecular Mechanisms of Diverse Activation Stimulated by Different Biased Agonists for the β2-Adrenergic Receptor. 5175-5192 - Rabindranath Paul
, Siddhartha Bera, Madhusmita Devi
, Sandip Paul
:
Inhibition of Aβ16-22 Peptide Aggregation by Small Molecules and Their Permeation through POPC Lipid Bilayer: Insight from Molecular Dynamics Simulation Study. 5193-5207 - Guoqin Feng, Xiangying Zhang, Yan Li
, Renxiao Wang
:
Analysis of the Binding Sites on BAX and the Mechanism of BAX Activators through Extensive Molecular Dynamics Simulations. 5208-5222 - Yunyuan Huang, Jiqun Wang, Jiaqi Liu, Donglei Shi
, Xiaokang Li, Manjiong Wang, Taotao Lu, Bei Jiang, Conglong Xia, Houwen Lin
, Yixiang Xu, Jian Li
:
Rapid Repurposing of Novel Combination Drugs for the Treatment of Heart Failure via a Computationally Guided Network Screening Approach. 5223-5232 - Haiyi Chen, Rui Zhou, Jinping Pang, Yue Guo, Jiawen Chen, Yu Kang, Mojie Duan
, Tingjun Hou
:
Molecular View on the Dissociation Pathways and Transactivation Regulation Mechanism of Nonsteroidal GR Ligands. 5233-5245 - Dongxiao Hao
, He Wang
, Yongjian Zang
, Lei Zhang
, Zhiwei Yang
, Shengli Zhang
:
Mechanism of Glycans Modulating Cholesteryl Ester Transfer Protein: Unveiled by Molecular Dynamics Simulation. 5246-5257 - Yibo Wang
, Siru Wu, Cong Zhang, Yushan Jin, Xiaohui Wang
:
Dissecting the Role of N-Glycan at N413 in Toll-like Receptor 3 via Molecular Dynamics Simulations. 5258-5266 - Wanqian Dong, Rui Zhou, Jiawen Chen, Zhengyu Shu, Mojie Duan
:
Phosphorylation Regulation on the Homo-Dimeric Binding of Transactive Response DNA-Binding Protein. 5267-5275 - Maywan Hariono
, Dominikus B. E. Wijaya, Teddy Chandra, Nico Frederick, Agnes B. Putri, Erlia Herawati, Luthfi A. Warastika, Merry Permatasari, Agata D. A. Putri, Satrio Ardyantoro:
A Decade of Indonesian Atmosphere in Computer-Aided Drug Design. 5276-5288 - Yunshuo Zhao, Xiaotong Chen, Zhe Ding, Chuanjie He, Guanfei Gao, Sifan Lyu, Yanfeng Gao
, Jiangfeng Du
:
Identification of Novel CD39 Inhibitors Based on Virtual Screening and Enzymatic Assays. 5289-5304 - Richa Mardianingrum, Maywan Hariono
, Ruswanto Ruswanto, Muhammad Yusuf
, Muchtaridi Muchtaridi
:
Synthesis, Anticancer Activity, Structure-Activity Relationship, and Molecular Modeling Studies of α-Mangostin Derivatives as hERα Inhibitor. 5305-5316
Volume 62, Number 22, November 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Thereza A. Soares
, Ariane Nunes-Alves
, Angelica Mazzolari
, Fiorella Ruggiu
, Guo-Wei Wei
, Kenneth M. Merz Jr.
:
The (Re)-Evolution of Quantitative Structure-Activity Relationship (QSAR) Studies Propelled by the Surge of Machine Learning Methods. 5317-5320 - Youjun Xu
, Jinchuan Xiao, Chia-Han Chou, Jianhang Zhang, Jintao Zhu, Qiwan Hu, Hemin Li, Ningsheng Han, Bingyu Liu, Shuaipeng Zhang, Jinyu Han, Zhen Zhang, Shuhao Zhang
, Weilin Zhang, Luhua Lai
, Jianfeng Pei
:
MolMiner: You Only Look Once for Chemical Structure Recognition. 5321-5328 - Fergus Boyles
, Charlotte M. Deane
, Garrett M. Morris
:
Learning from Docked Ligands: Ligand-Based Features Rescue Structure-Based Scoring Functions When Trained on Docked Poses. 5329-5341 - Connor J. Morris
, Jacob A. Stern, Brenden Stark, Max Christopherson, Dennis Della Corte
:
MILCDock: Machine Learning Enhanced Consensus Docking for Virtual Screening in Drug Discovery. 5342-5350 - Tatsuya Yoshizawa
, Shoichi Ishida
, Tomohiro Sato
, Masateru Ohta
, Teruki Honma
, Kei Terayama
:
Selective Inhibitor Design for Kinase Homologs Using Multiobjective Monte Carlo Tree Search. 5351-5360 - Zewei Ji
, Runhan Shi, Jiarui Lu, Fang Li, Yang Yang
:
ReLMole: Molecular Representation Learning Based on Two-Level Graph Similarities. 5361-5372 - Zhen Liu
, Tetiana Zubatiuk, Adrian E. Roitberg
, Olexandr Isayev
:
Auto3D: Automatic Generation of the Low-Energy 3D Structures with ANI Neural Network Potentials. 5373-5382 - Oliver B. Scott, Jing Gu, A. W. Edith Chan
:
Classification of Protein-Binding Sites Using a Spherical Convolutional Neural Network. 5383-5396 - Joshua L. Lansford
, Brian C. Barnes, Betsy M. Rice
, Klavs F. Jensen
:
Building Chemical Property Models for Energetic Materials from Small Datasets Using a Transfer Learning Approach. 5397-5410 - Rodrigo S. Hormazabal
, Jeong Won Kang
, Kiho Park
, Dae Ryook Yang:
Not from Scratch: Predicting Thermophysical Properties through Model-Based Transfer Learning Using Graph Convolutional Networks. 5411-5424 - Alberto Celma
, Richard Bade
, Juan Vicente Sancho, Félix Hernandez
, Melissa Humphries, Lubertus Bijlsma
:
Prediction of Retention Time and Collision Cross Section (CCSH+, CCSH-, and CCSNa+) of Emerging Contaminants Using Multiple Adaptive Regression Splines. 5425-5434 - Evan R. Antoniuk
, Peggy Li, Bhavya Kailkhura, Anna M. Hiszpanski
:
Representing Polymers as Periodic Graphs with Learned Descriptors for Accurate Polymer Property Predictions. 5435-5445 - Pin Chen
, Rui Jiao, Jinyu Liu, Yang Liu, Yutong Lu:
Interpretable Graph Transformer Network for Predicting Adsorption Isotherms of Metal-Organic Frameworks. 5446-5456 - Kaycee Low, Michelle L. Coote
, Ekaterina I. Izgorodina
:
Explainable Solvation Free Energy Prediction Combining Graph Neural Networks with Chemical Intuition. 5457-5470 - William Bort, Daniyar Mazitov
, Dragos Horvath
, Fanny Bonachéra, Arkadii I. Lin, Gilles Marcou
, Igor I. Baskin
, Timur I. Madzhidov
, Alexandre Varnek
:
Inverse QSAR: Reversing Descriptor-Driven Prediction Pipeline Using Attention-Based Conditional Variational Autoencoder. 5471-5484 - Hui Zhu
, Jincai Yang
, Niu Huang
:
Assessment of the Generalization Abilities of Machine-Learning Scoring Functions for Structure-Based Virtual Screening. 5485-5502 - João Paulo Almeida de Mendonça
, Felipe V. Calderan
, Tuanan C. Lourenço
, Marcos G. Quiles
, Juarez L. F. Da Silva
:
Theoretical Framework Based on Molecular Dynamics and Data Mining Analyses for the Study of Potential Energy Surfaces of Finite-Size Particles. 5503-5512 - Jakob L. Andersen
, Rolf Fagerberg
, Christoph Flamm
, Walter Fontana
, Juraj Kolcák, Christophe V. F. P. Laurent
, Daniel Merkle
, Nikolai Nøjgaard:
Representing Catalytic Mechanisms with Rule Composition. 5513-5524 - Bas van Beek, Juliette Zito
, Lucas Visscher
, Ivan Infante
:
CAT: A Compound Attachment Tool for the Construction of Composite Chemical Compounds. 5525-5535 - Sonia Ziada, Julien Diharce
, Eric Raimbaud, Samia Aci-Sèche
, Pierre Ducrot, Pascal Bonnet
:
Estimation of Drug-Target Residence Time by Targeted Molecular Dynamics Simulations. 5536-5549 - Yanjun Li
, Daohong Zhou, Guangrong Zheng
, Xiaolin Li, Dapeng Wu, Yaxia Yuan
:
DyScore: A Boosting Scoring Method with Dynamic Properties for Identifying True Binders and Nonbinders in Structure-Based Drug Discovery. 5550-5567 - Iñigo Iribarren
, Cristina Trujillo
:
Efficiency and Suitability when Exploring the Conformational Space of Phase-Transfer Catalysts. 5568-5580 - Xin Chen
, Yuan Yuan, Yichi Chen, Jin Yu
, Jingzhou Wang, Jianfang Chen, Yanzhi Guo, Xuemei Pu
:
Biased Activation Mechanism Induced by GPCR Heterodimerization: Observations from μOR/δOR Dimers. 5581-5600 - Robert J. Cordina
, Beccy Smith, Tell Tuttle
:
Rapid Automated Quantification of Triacylglyceride Crystallinity in Molecular Dynamics Simulations. 5601-5606 - Soumyo Sen, Aleksandar Spasic, Anjana Sinha, Jialing Wang, Martin Bush, Jihong Li, Dragana Nesic, Yuchen Zhou, Gabriella Angiulli, Paul Morgan
, Leslie Salas-Estrada, Junichi Takagi, Thomas Walz
, Barry S. Coller
, Marta Filizola
:
Structure-Based Discovery of a Novel Class of Small-Molecule Pure Antagonists of Integrin αVβ3. 5607-5621 - Joshua T. Horton
, Simon Boothroyd, Jeffrey Wagner, Joshua A. Mitchell, Trevor Gokey, David L. Dotson, Pavan Kumar Behara
, Venkata Krishnan Ramaswamy, Mark Mackey
, John D. Chodera
, Jamshed Anwar
, David L. Mobley, Daniel J. Cole
:
Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale. 5622-5633 - Tom Frömbgen
, Jan Blasius
, Vahideh Alizadeh
, Alain Chaumont
, Martin Brehm
, Barbara Kirchner
:
Cluster Analysis in Liquids: A Novel Tool in TRAVIS. 5634-5644 - Wenlang Liu, Zhenhao Liu, Hao Liu, Lance M. Westerhoff
, Zheng Zheng
:
Free Energy Calculations Using the Movable Type Method with Molecular Dynamics Driven Protein-Ligand Sampling. 5645-5665 - Austin M. Cool, Steffen Lindert
:
Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin. 5666-5674 - Eric R. Hantz
, Steffen Lindert
:
Actives-Based Receptor Selection Strongly Increases the Success Rate in Structure-Based Drug Design and Leads to Identification of 22 Potent Cancer Inhibitors. 5675-5687 - Yanru Ji, Ying Fang, Jianhua Wu
:
Tension Enhances the Binding Affinity of β1 Integrin by Clamping Talin Tightly: An Insight from Steered Molecular Dynamics Simulations. 5688-5698 - Keigo Gohda
:
Conformational Analysis of the Loop-to-Helix Transition of the α-Helix3 Plastic Region in the N-Terminal Domain of Human Hsp90α by a Computational Biochemistry Approach. 5699-5714 - Matteo Pavan
, Silvia Menin
, Davide Bassani
, Mattia Sturlese
, Stefano Moro
:
Qualitative Estimation of Protein-Ligand Complex Stability through Thermal Titration Molecular Dynamics Simulations. 5715-5728 - Jiao Zhou
, Wei Li, Shanyue Guan, Xiaohong Chen, Xiang Liu
, Weiyan Shao:
Discovery of Chemokine CXCL12 Inhibitors by Tandem Application of Virtual Screening and NMR Spectrometry. 5729-5737 - Xavier Daura
, Oscar Conchillo-Solé
:
On Quality Thresholds for the Clustering of Molecular Structures. 5738-5745 - Vinicius Gonçalves Maltarollo, Ekaterina Shevchenko, Igor Daniel de Miranda Lima, Elio A. Cino, Glaucio Monteiro Ferreira
, Antti Poso
, Thales Kronenberger
:
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels. 5746-5761 - Tingting Fu, Hongxing Zhang
, Qingchuan Zheng
:
Molecular Insights into the Heterotropic Allosteric Mechanism in Cytochrome P450 3A4-Mediated Midazolam Metabolism. 5762-5770 - Nil Casajuana-Martin, Gemma Navarro, Angel Gonzalez
, Claudia Llinas del Torrent
, Marc Gómez-Autet, Aleix Quintana García
, Rafael Franco
, Leonardo Pardo
:
A Single Point Mutation Blocks the Entrance of Ligands to the Cannabinoid CB2 Receptor via the Lipid Bilayer. 5771-5779 - Ying Wang
, Huan Wang, Yupeng Zhang, Feng Xu, Jian Wang
, Fengjiao Zhang
:
Stepwise Strategy to Identify Thrombin as a Hydrolytic Substrate for Nattokinase. 5780-5793 - Francesca Picarazzi
, Marika Zuanon, Gaia Pasqualetto, Silvia Cammarone
, Isabella Romeo, Mark T. Young
, Andrea Brancale
, Marcella Bassetto
, Mattia Mori
:
Identification of Small Molecular Chaperones Binding P23H Mutant Opsin through an In Silico Structure-Based Approach. 5794-5805 - Jinze Zhang, Hao Li, Xuejun Zhao, Qilong Wu
, Sheng-You Huang
:
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement. 5806-5820 - Janez Konc
, Dusanka Janezic
:
ProBiS-Fold Approach for Annotation of Human Structures from the AlphaFold Database with No Corresponding Structure in the PDB to Discover New Druggable Binding Sites. 5821-5829 - Ruihan Dong
, Hongpeng Yang, Chengwei Ai, Guihua Duan, Jianxin Wang, Fei Guo:
DeepBLI: A Transferable Multichannel Model for Detecting β-Lactamase-Inhibitor Interaction. 5830-5840 - Bailu Yan
, Xinchun Ran, Anvita Gollu, Zihao Cheng, Xiang Zhou
, Yiwen Chen, Zhongyue J. Yang
:
IntEnzyDB: an Integrated Structure-Kinetics Enzymology Database. 5841-5848
Volume 62, Number 23, December 2022
- Martin J. Field
:
pDynamo3 Molecular Modeling and Simulation Program. 5849-5854 - Georgios Iakovou, Stephen D. Laycock
, Steven Hayward
:
Interactive Flexible-Receptor Molecular Docking in Virtual Reality Using DockIT. 5855-5861 - Xiujuan Ou, Yi Zhang, Yiduo Xiong, Yi Xiao
:
Advances in RNA 3D Structure Prediction. 5862-5874 - Minjie Mou
, Ziqi Pan
, Mingkun Lu
, Huaicheng Sun
, Yunxia Wang
, Yongchao Luo
, Feng Zhu
:
Application of Machine Learning in Spatial Proteomics. 5875-5895 - Eugene Raush, Ruben Abagyan
, Maxim Totrov
:
Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules. 5896-5906 - Youhai Tan
, Lingxue Dai, Weifeng Huang, Yinfeng Guo, Shuangjia Zheng
, Jinping Lei
, Hongming Chen, Yuedong Yang
:
DRlinker: Deep Reinforcement Learning for Optimization in Fragment Linking Design. 5907-5917 - Ravithree D. Senanayake
, Xiaoxiao Yao
, Clarice E. Froehlich
, Meghan S. Cahill
, Trever R. Sheldon
, Mary McIntire
, Christy L. Haynes
, Rigoberto Hernandez
:
Machine Learning-Assisted Carbon Dot Synthesis: Prediction of Emission Color and Wavelength. 5918-5928 - Lei Deng, Ziyu Fan, Xiaojun Xiao, Hui Liu
, Jiaxuan Zhang:
Dual-Channel Heterogeneous Graph Neural Network for Predicting microRNA-Mediated Drug Sensitivity. 5929-5937 - Derek van Tilborg, Alisa Alenicheva
, Francesca Grisoni
:
Exposing the Limitations of Molecular Machine Learning with Activity Cliffs. 5938-5951 - Youngchun Kwon, Sun Kim, Youn-Suk Choi
, Seokho Kang
:
Generative Modeling to Predict Multiple Suitable Conditions for Chemical Reactions. 5952-5960 - Shuang Wang, Wenqi Chen
, Peifu Han, Xue Li, Tao Song:
RGN: Residue-Based Graph Attention and Convolutional Network for Protein-Protein Interaction Site Prediction. 5961-5974 - Jialu Wu, Junmei Wang
, Zhenxing Wu, Shengyu Zhang, Yafeng Deng, Yu Kang
, Dong-Sheng Cao
, Chang-Yu Hsieh
, Tingjun Hou
:
ALipSol: An Attention-Driven Mixture-of-Experts Model for Lipophilicity and Solubility Prediction. 5975-5987 - Satoshi Noguchi
, Junya Inoue:
Exploration of Chemical Space Guided by PixelCNN for Fragment-Based De Novo Drug Discovery. 5988-6001 - Maximilian Beckers
, Nikolas Fechner
, Nikolaus Stiefl
:
25 Years of Small-Molecule Optimization at Novartis: A Retrospective Analysis of Chemical Series Evolution. 6002-6021 - Xiaowen Dai
, Yuan Xu, Haodi Qiu, Xu Qian, Mingde Lin, Lin Luo, Yang Zhao, Dingfang Huang, Yanmin Zhang
, Yadong Chen
, Haichun Liu, Yulei Jiang:
KID: A Kinase-Focused Interaction Database and Its Application in the Construction of Kinase-Focused Molecule Databases. 6022-6034 - Xia Zhao, Yuhao Sun, Ruiqiu Zhang, Zhaoyang Chen, Yuqing Hua, Pei Zhang, Huizhu Guo, Xueyan Cui, Xin Huang, Xiao Li
:
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity. 6035-6045 - Fan Hu
, Dongqi Wang, Huazhen Huang, Yishen Hu, Peng Yin
:
Bridging the Gap between Target-Based and Cell-Based Drug Discovery with a Graph Generative Multitask Model. 6046-6056 - Xiao-Kang Guo, Yingkai Zhang
:
CovBinderInPDB: A Structure-Based Covalent Binder Database. 6057-6068 - Abir Ganguly
, Hsu-Chun Tsai
, Mario Fernández-Pendás
, Tai-Sung Lee
, Timothy J. Giese
, Darrin M. York
:
AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA). 6069-6083 - Han Zhang
, Seonghoon Kim
, Wonpil Im
:
Practical Guidance for Consensus Scoring and Force Field Selection in Protein-Ligand Binding Free Energy Simulations. 6084-6093 - Lorenzo D'amore
, David F. Hahn, David L. Dotson, Joshua T. Horton
, Jamshed Anwar
, Ian Craig, Thomas Fox
, Alberto Gobbi
, Sirish Kaushik Lakkaraju
, Xavier Lucas
, Katharina Meier, David L. Mobley, Arjun Narayanan, Christina E. M. Schindler
, William C. Swope
, Pieter J. in 't Veld
, Jeffrey Wagner, Bai Xue
, Gary Tresadern
:
Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field. 6094-6104 - Jelena Tosovic
, Domagoj Fijan
, Marko Jukic
, Urban Bren
:
Conserved Water Networks Identification for Drug Design Using Density Clustering Approaches on Positional and Orientational Data. 6105-6117 - Jianzhong Chen
, Qingkai Zeng, Wei Wang, Haibo Sun, Guodong Hu:
Decoding the Identification Mechanism of an SAM-III Riboswitch on Ligands through Multiple Independent Gaussian-Accelerated Molecular Dynamics Simulations. 6118-6132 - Perumal Manivel, Parthiban Marimuthu
, Sun Yu, Xiumin Chen
:
Multispectroscopic and Computational Investigations on the Binding Mechanism of Dicaffeoylquinic Acids with Ovalbumin. 6133-6147 - Tianyi Yang
, Li Han
, Shuanghong Huo
:
Dynamics and Allosteric Information Pathways of Unphosphorylated c-Cbl. 6148-6159 - Lin Wang, Fenglei Li, Xin-yue Ma, Yong Cang, Fang Bai
:
PPI-Miner: A Structure and Sequence Motif Co-Driven Protein-Protein Interaction Mining and Modeling Computational Method. 6160-6171 - Yang Zhou
, Junhao Li, Glib Baryshnikov
, Yaoquan Tu
:
Unraveling the Abnormal Molecular Mechanism of Suicide Inhibition of Cytochrome P450 3A4. 6172-6181 - Klaudia Mráziková
, Holger Kruse
, Vojtech Mlýnský
, Pascal Auffinger
, Jirí Sponer
:
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions. 6182-6200 - Eric R. Hantz
, Steffen Lindert
:
Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C. 6201-6208 - Dominykas Lukauskis
, Marley L. Samways
, Simone Aureli, Benjamin P. Cossins, Richard D. Taylor
, Francesco Luigi Gervasio
:
Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein-Ligand Binding Poses. 6209-6216 - Takunori Yasuda, Rikuri Morita
, Yasuteru Shigeta
, Ryuhei Harada
:
Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace. 6217-6227 - James Vergilio, Christopher Lockhart
, Dmitri K. Klimov
:
De Novo Transmembrane Aggregation of Aβ10-40 Peptides in an Anionic Lipid Bilayer. 6228-6241 - Andreas Denger
, Volkhard Helms
:
Optimized Data Set and Feature Construction for Substrate Prediction of Membrane Transporters. 6242-6257 - Deng Pan, Lijun Quan
, Zhi Jin, Taoning Chen, Xuejiao Wang, Jingxin Xie, Tingfang Wu, Qiang Lyu:
Multisource Attention-Mechanism-Based Encoder-Decoder Model for Predicting Drug-Drug Interaction Events. 6258-6270 - Zhenqiu Shu
, Qinghan Long, Luping Zhang, Zhengtao Yu, Xiao-Jun Wu:
Robust Graph Regularized NMF with Dissimilarity and Similarity Constraints for ScRNA-seq Data Clustering. 6271-6286
Volume 62, Number 24, December 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Zoe Cournia
, Thereza A. Soares
, Habibah A. Wahab
, Rommie E. Amaro
:
Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry. 6287-6291 - Chrystal D. Bruce
, Patricia M. Flatt, Sarah R. Kirk
, Elizabeth Roberts-Kirchhoff, Hala G. Schepmann:
The Value of Peer Mentoring Networks for Developing Leaders and Inspiring Change. 6292-6296 - Michele Cascella
, Thereza A. Soares
:
Bias Amplification in Gender, Gender Identity, and Geographical Affiliation. 6297-6301 - Yuxiang Wang
, Alper Kiziltas, Patrick Blanchard, Tiffany R. Walsh
:
ContactAngleCalculator: An Automated, Parametrized, and Flexible Code for Contact Angle Estimation in Visual Molecular Dynamics. 6302-6308 - Deborah Palazzotti
, Martina Fiorelli, Stefano Sabatini
, Serena Massari
, Maria Letizia Barreca
, Andrea Astolfi
:
Q-raKtion: A Semiautomated KNIME Workflow for Bioactivity Data Points Curation. 6309-6315 - Kelly Anderson
, Sarah Arradondo
, K. Aurelia Ball
, Chrystal D. Bruce
, Maria A. Gomez
, Kedan He
, Heidi Hendrickson
, Lindsey Madison, Ashley Ringer McDonald
, Maria C. Nagan
, Caitlin E. Scott, Patricia Soto
, Aimée Tomlinson
, Mychel Varner, Carol A. Parish
:
The Impacts of the Molecular Education and Research Consortium in Undergraduate Computational Chemistry on the Careers of Women in Computational Chemistry. 6316-6322 - Alzbeta Türková
, Brandon J. Bongers
, Ulf Norinder
, Orsolya Ungvári, Virág Székely, Andrey Tarnovskiy, Gergely Szakács, Csilla Özvegy-Laczka, Gerard J. P. van Westen
, Barbara Zdrazil
:
Identifying Novel Inhibitors for Hepatic Organic Anion Transporting Polypeptides by Machine Learning-Based Virtual Screening. 6323-6335 - Megan A. Lim, Song Yang, Huanghao Mai, Alan C. Cheng
:
Exploring Deep Learning of Quantum Chemical Properties for Absorption, Distribution, Metabolism, and Excretion Predictions. 6336-6341 - María Jimena Martínez
, María Virginia Sabando
, Axel J. Soto
, Carlos Roca
, Carlos Requena-Triguero
, Nuria E. Campillo
, Juan A. Páez, Ignacio Ponzoni
:
Multitask Deep Neural Networks for Ames Mutagenicity Prediction. 6342-6351 - Rangsiman Ketkaew
, Sandra Luber
:
DeepCV: A Deep Learning Framework for Blind Search of Collective Variables in Expanded Configurational Space. 6352-6364 - Shu Huang
, Jacqueline M. Cole
:
BatteryBERT: A Pretrained Language Model for Battery Database Enhancement. 6365-6377 - Swati Baskiyar, Chang Ren, Kabre L. Heck, Audrey M. Hall, Muhammad Gulfam, Sadaira Packer, Cheryl D. Seals, Angela I. Calderón
:
Bioactive Natural Products Identification Using Automation of Molecular Networking Software. 6378-6385 - Neetu Tripathi, Manoj Kumar Goshisht
:
Advancing Women in Chemistry: A Step Toward Gender Parity. 6386-6397 - Marko Babic
, Patrizia Jankovic
, Silvia Marchesan
, Goran Mausa
, Daniela Kalafatovic
:
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs. 6398-6410 - Soma Roy, Santanu Bhattacharya
:
Chemical Information and Computational Modeling of Targeting Hybrid Nucleic Acid Structures of PIM1 Sequences by Synthetic Pyrrole-Imidazole Carboxamide Drugs. 6411-6422 - Juan Antonio Seijas-Bellido, Bipasa Samanta, Karen Valadez-Villalobos, Juan Jesús Gallardo
, Javier Navas
, Salvador R. G. Balestra
, Rafael María Madero Castro
, José Manuel Vicent-Luna
, Shuxia Tao
, Maytal Caspary Toroker
, Juan Antonio Anta
:
Transferable Classical Force Field for Pure and Mixed Metal Halide Perovskites Parameterized from First-Principles. 6423-6435 - Christina Eleftheria Tzeliou, Demeter Tzeli
:
3-Input AND Molecular Logic Gate with Enhanced Fluorescence Output: The Key Atom for the Accurate Prediction of the Spectra. 6436-6448 - Shruti Koulgi
, Archana Achalere
, Uddhavesh Sonavane
, Rajendra Joshi
:
Markov State Modeling Analysis Captures Changes in the Temperature-Sensitive N-Terminal and β-Turn Regions of the p53 DNA-Binding Domain. 6449-6461 - Milla Kurki
, Antti Poso
, Piia Bartos
, Markus S. Miettinen
:
Structure of POPC Lipid Bilayers in OPLS3e Force Field. 6462-6474 - Jay-Anne K. Johnson, Isaiah Sumner
:
On the Possibility That Bond Strain Is the Mechanism of RING E3 Activation in the E2-Catalyzed Ubiquitination Reaction. 6475-6481 - Ke Wang, Xueguang Shao
, Wensheng Cai
:
Binding Models of Aβ42 Peptide with Membranes Explored by Molecular Simulations. 6482-6493 - María Lucrecia Bogado
, Roxana Noelia Villafañe, José Leonardo Gómez Chavez, Emilio Luis Angelina
, Gladis Laura Sosa, Nélida María Peruchena:
Targeting Protein Pockets with Halogen Bonds: The Role of the Halogen Environment. 6494-6507 - Paptawan Thongdee
, Chayanin Hanwarinroj
, Bongkochawan Pakamwong
, Pharit Kamsri
, Auradee Punkvang
, Jiraporn Leanpolchareanchai, Sombat Ketrat
, Patchreenart Saparpakorn
, Supa Hannongbua
, Kanchiyaphat Ariyachaokun
, Khomson Suttisintong
, Sanya Sureram
, Prasat Kittakoop
, Poonpilas Hongmanee
, Pitak Santanirand, Galina V. Mukamolova, Rosemary A. Blood, Yuiko Takebayashi
, James Spencer
, Adrian J. Mulholland
, Pornpan Pungpo
:
Virtual Screening Identifies Novel and Potent Inhibitors of Mycobacterium tuberculosis PknB with Antibacterial Activity. 6508-6518 - Alexandra V. Krivitskaya
, Maria G. Khrenova
:
Interplay between the Enamine and Imine Forms of the Hydrolyzed Imipenem in the Active Sites of Metallo-β-lactamases and in Water Solution. 6519-6529 - Alexsander C. Vendite
, Thereza A. Soares
, Kaline Coutinho
:
The Effect of Surface Composition on the Selective Capture of Atmospheric CO2 by ZIF Nanoparticles: The Case of ZIF-8. 6530-6543 - Akie Kowaguchi
, Katsuhiro Endo
, Paul E. Brumby
, Kentaro Nomura, Kenji Yasuoka
:
Optimal Replica-Exchange Molecular Simulations in Combination with Evolution Strategies. 6544-6552 - Lucianna Helene Santos, Thales Kronenberger
, Renata G. Almeida, Elany B. Silva
, Rafael E. O. Rocha, Joyce C. Oliveira, Luiza V. Barreto, Danielle Skinner, Pavla Fajtová
, Miriam A. Giardini
, Brendon Woodworth, Conner Bardine
, André L. Lourenço
, Charles S. Craik
, Antti Poso
, Larissa M. Podust
, James H. McKerrow
, Jair L. Siqueira-Neto
, Anthony J. O'Donoghue
, Eufrânio N. da Silva Júnior
, Rafaela Salgado Ferreira
:
Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease Mpro and Papain-like Protease PLpro of SARS-CoV-2. 6553-6573 - Gaurav Sharma
, Lin Frank Song, Kenneth M. Merz Jr.
:
Effect of an Inhibitor on the ACE2-Receptor-Binding Domain of SARS-CoV-2. 6574-6585 - Marius T. Wenz
, Miriam Bertazzon, Jana Sticht, Stevan Aleksic, Daniela Gjorgjevikj, Christian Freund, Bettina G. Keller
:
Target Recognition in Tandem WW Domains: Complex Structures for Parallel and Antiparallel Ligand Orientation in h-FBP21 Tandem WW. 6586-6601 - Emmanuel E. Moutoussamy, Hanif M. Khan
, Mary F. Roberts
, Anne Gershenson
, Christophe Chipot
, Nathalie Reuter
:
Standard Binding Free Energy and Membrane Desorption Mechanism for a Phospholipase C. 6602-6613 - Agustín Ormazábal, Gustavo Pierdominici-Sottile
, Juliana Palma
:
Recognition and Binding of RsmE to an AGGAC Motif of RsmZ: Insights from Molecular Dynamics Simulations. 6614-6627 - Sree Kavya Penneru
, Moumita Saharay
, Marimuthu Krishnan
:
CelS-Catalyzed Processive Cellulose Degradation and Cellobiose Extraction for the Production of Bioethanol. 6628-6638 - Yongjian Zang
, He Wang
, Dongxiao Hao
, Ying Kang, Jianwen Zhang, Xuhua Li, Lei Zhang
, Zhiwei Yang
, Shengli Zhang:
p38α Kinase Auto-Activation through Its Conformational Transition Induced by Tyr323 Phosphorylation. 6639-6648 - Krystel El Hage
, Giovanni Ribaudo
, Louis Lagardère
, Alberto Ongaro, Philippe H. Kahn, Luc Demange, Jean-Philip Piquemal
, Giuseppe Zagotto
, Nohad Gresh
:
Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators. 6649-6666 - Shuangyan Zhou
, Huizhen Zou, Yu Wang, Glenn V. Lo, Shuai Yuan
:
Atomic Mechanisms of Transthyretin Tetramer Dissociation Studied by Molecular Dynamics Simulations. 6667-6678 - Shalini Yadav
, Vandana Kardam, Ankita Tripathi, Shruti T. G, Kshatresh Dutta Dubey
:
The Performance of Different Water Models on the Structure and Function of Cytochrome P450 Enzymes. 6679-6690 - Riccardo Rozza
, Andrea Saltalamacchia
, Clarissa Orrico, Pavel Janos
, Alessandra Magistrato
:
All-Atom Simulations Elucidate the Impact of U2AF2 Cancer-Associated Mutations on Pre-mRNA Recognition. 6691-6703 - Jozica Dolenc
, Esme J. Haywood, Tingting Zhu, Lorna J. Smith
:
Backbone N-Amination Promotes the Folding of β-Hairpin Peptides via a Network of Hydrogen Bonds. 6704-6714 - Ebru Çetin
, Ali Rana Atilgan
, Canan Atilgan
:
DHFR Mutants Modulate Their Synchronized Dynamics with the Substrate by Shifting Hydrogen Bond Occupancies. 6715-6726 - Lei Chen, Weikang Gong
, Zhongjie Han
, Wenxue Zhou, Shuang Yang, Chunhua Li
:
Key Residues in δ Opioid Receptor Allostery Explored by the Elastic Network Model and the Complex Network Model Combined with the Perturbation Method. 6727-6738 - Alessio Bartocci
, Gilberto Pereira, Marco Cecchini
, Elise Dumont
:
Capturing the Recognition Dynamics of para-Sulfonato-calix[4]arenes by Cytochrome c: Toward a Quantitative Free Energy Assessment. 6739-6748 - Sharon Emily Stone, Dhiman Ray
, Ioan Andricioaei:
Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA. 6749-6761 - Huiyan Lu, Yuji Komukai, Koto Usami, Yan Guo, Xinyue Qiao, Michiyoshi Nukaga, Tyuji Hoshino
:
Computational and Crystallographic Analysis of Binding Structures of Inhibitory Compounds for HIV-1 RNase H Activity. 6762-6774 - Volkan Findik
, Betül Tuba Varinca Gerçik, Öykü Sinek, Safiye Sag Erdem
, Manuel F. Ruiz-López
:
Mechanistic Investigation of Lysine-Targeted Covalent Inhibition of PI3Kδ via ONIOM QM: QM Computations. 6775-6787 - Lisbeth Ravnkilde Kjølbye
, Lars Sørensen, Jun Yan
, Nils A. Berglund, Jesper Ferkinghoff-Borg, Carol V. Robinson
, Birgit Schiøtt
:
Lipid Modulation of a Class B GPCR: Elucidating the Modulatory Role of PI(4, 5)P2 Lipids. 6788-6802 - Karolina Mitusinska
, Maria Bzówka
, Tomasz Magdziarz, Artur Góra
:
Geometry-Based versus Small-Molecule Tracking Method for Tunnel Identification: Benefits and Pitfalls. 6803-6811 - Daniela Trisciuzzi, Lydia Siragusa
, Massimo Baroni, Gabriele Cruciani, Orazio Nicolotti
:
An Integrated Machine Learning Model To Spot Peptide Binding Pockets in 3D Protein Screening. 6812-6824 - Melina Mottin, Bruna Katiele de Paula Sousa
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Discovery of New Zika Protease and Polymerase Inhibitors through the Open Science Collaboration Project OpenZika. 6825-6843 - Brandon Úsuga-Acevedo
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Rational Discovery of Microtubule-Stabilizing Peptides. 6844-6856
![](https://dblp1.uni-trier.de/img/cog.dark.24x24.png)
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