


Остановите войну!
for scientists:


default search action
Journal of Chemical Information and Modeling, Volume 63
Volume 63, Number 1, January 2023
- Issue Publication Information.
- Issue Editorial Masthead.
- Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
:
Editorial: Machine Learning in Bio-cheminformatics. 1 - Martin Stroet
, Stephen Sanderson
, Audrey V. Sanzogni, Sharif Nada, Thomas Lee
, Bertrand Caron, Alan E. Mark
, Paul L. Burn
:
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies. 2-8 - Ahmet Yildirim, Mustafa Tekpinar
:
Building Quantitative Bridges between Dynamics and Sequences of SARS-CoV-2 Main Protease and a Diverse Set of Thirty-Two Proteins. 9-19 - Rui P. P. Neves
, Maria João Ramos
, Pedro Alexandrino Fernandes
:
Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis. 20-26 - Daniel Vella
, Jean-Paul Ebejer
:
Few-Shot Learning for Low-Data Drug Discovery. 27-42 - Weimin Zhu, Yi Zhang, Duancheng Zhao, Jianrong Xu, Ling Wang
:
HiGNN: A Hierarchical Informative Graph Neural Network for Molecular Property Prediction Equipped with Feature-Wise Attention. 43-55 - Maria Vittoria Togo, Fabrizio Mastrolorito, Fulvio Ciriaco, Daniela Trisciuzzi, Anna Rita Tondo, Nicola Gambacorta, Loredana Bellantuono
, Alfonso Monaco, Francesco Leonetti, Roberto Bellotti, Cosimo Damiano Altomare, Nicola Amoroso, Orazio Nicolotti
:
TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity. 56-66 - Hao Tian
, Xi Jiang, Sian Xiao
, Hunter La Force, Eric C. Larson, Peng Tao
:
LAST: Latent Space-Assisted Adaptive Sampling for Protein Trajectories. 67-75 - Ryo Kawada
, Katsuhiro Endo
, Kenji Yasuoka
, Hidekazu Kojima, Nobuyuki Matubayasi
:
Prediction of Water Diffusion in Wide Varieties of Polymers with All-Atom Molecular Dynamics Simulations and Deep Generative Models. 76-86 - Omer Kaspi, Osnat Israelsohn-Azulay, Zidon Yigal, Hila Rosengarten, Matea Krmpotic
, Sabrina Gouasmia, Iva Bogdanovic-Radovic
, Pasi Jalkanen, Anna Liski, Kenichiro Mizohata, Jyrki Räisänen, Zsolt Kasztovszky, Ildikó Harsányi, Raghunath Acharya, Pradeep K. Pujari
, Molnár Mihály, Mihaly Braun, Nahum Shabi, Olga Girshevitz, Hanoch Senderowitz
:
Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments. 87-100 - Jörg Heider, Jonas Kilian, Aleksandra Garifulina, Steffen Hering, Thierry Langer
, Thomas Seidel
:
Apo2ph4: A Versatile Workflow for the Generation of Receptor-based Pharmacophore Models for Virtual Screening. 101-110 - Teng-Zhi Long
, Shao-Hua Shi
, Shao Liu, Ai-Ping Lu, Zhao-Qian Liu
, Min Li
, Tingjun Hou
, Dong-Sheng Cao
:
Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches. 111-125 - Omri Wolk
, Amiram Goldblum
:
Predicting the Likelihood of Molecules to Act as Modulators of Protein-Protein Interactions. 126-137 - Daniel Sethio
, Poongavanam Vasanthanathan
, Ruisheng Xiong, Mohit Tyagi, Duc Duy Vo, Roland Lindh
, Jan Kihlberg
:
Simulation Reveals the Chameleonic Behavior of Macrocycles. 138-146 - Paul L. Türtscher, Markus Reiher
:
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach. 147-160 - Mirko Paulikat
, Daniele Vitone, Florian Karl Schackert
, Nils Schuth, Alessandra Barbanente, GiovanniMaria Piccini, Emiliano Ippoliti
, Giulia Rossetti
, Adam H. Clark
, Maarten Nachtegaal
, Michael Haumann, Holger Dau
, Paolo Carloni
, Silvano Geremia
, Rita De Zorzi, Liliana Quintanar
, Fabio Arnesano
:
Molecular Dynamics and Structural Studies of Zinc Chloroquine Complexes. 161-172 - Chen Qian, Xin Zhou, Jessica Rehmel, James P. Steele, Kjell A. Svensson, James P. Beck, Erik J. Hembre, Junliang Hao
:
Ensemble Docking Approach to Mitigate Pregnane X Receptor-Mediated CYP3A4 Induction Risk. 173-186 - Andrey I. Frolov
, Sunay V. Chankeshwara
, Zeyed Abdulkarim
, Gian Marco Ghiandoni
:
pIChemiSt ─ Free Tool for the Calculation of Isoelectric Points of Modified Peptides. 187-196 - Oriol Gracia Carmona
, Chris Oostenbrink
:
Accelerated Enveloping Distribution Sampling (AEDS) Allows for Efficient Sampling of Orthogonal Degrees of Freedom. 197-207 - Chythra J. N.
, Sairam S. Mallajosyula
:
Impact of Polarization on the Ring Puckering Dynamics of Hexose Monosaccharides. 208-223 - Nibedita Ray Chaudhuri, Shubhra Ghosh Dastidar
:
Allosteric Boost by TAB1 on the TAK1 Kinase Favorably Sculpts the Thermodynamic Landscape of Activation. 224-239 - Kei Moritsugu
, Toru Ekimoto, Mitsunori Ikeguchi
, Akinori Kidera:
Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease. 240-250 - Francesco Pettini
, Carmen Domene
, Simone Furini
:
Early Steps in C-Type Inactivation of the hERG Potassium Channel. 251-258 - Ryuhei Harada
, Rikuri Morita
, Yasuteru Shigeta
:
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods. 259-269 - Leslie Sánchez
, Fabiola E. Medina
, Fernanda Mendoza
, Camilo Febres-Molina, Gonzalo A. Jaña
:
Elucidation of the Reaction Mechanism of Cavia porcellus l-Asparaginase: A QM/MM Study. 270-280 - Till El Harrar
, Holger Gohlke
:
Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. 281-298 - Anastasiia Delova, Raúl Losantos
, Jérémy Pecourneau, Yann Bernhard, Maxime Mourer
, Andreea Pasc
, Antonio Monari
:
Perturbation of Lipid Bilayers by Biomimetic Photoswitches Based on Cyclocurcumin. 299-307 - Yuying Liu, Ying Wang, Yu Zhang, Yu Zou, Guanghong Wei
, Feng Ding
, Yunxiang Sun
:
Structural Perturbation of Monomers Determines the Amyloid Aggregation Propensity of Calcitonin Variants. 308-320 - Aristarc Suriñach, Adam Hospital
, Yvonne Westermaier
, Luis Jordà, Sergi Orozco-Ruiz, Daniel Beltrán, Francesco Colizzi
, Pau Andrio, Robert Soliva, Martí Municoy, Josep Lluis Gelpí, Modesto Orozco
:
High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic Simulations. 321-334 - Jiahui Chen
, Rui Wang
, Yuta Hozumi, Gengzhuo Liu, Yuchi Qiu, Xiaoqi Wei, Guo-Wei Wei
:
Emerging Dominant SARS-CoV-2 Variants. 335-342 - Luca Torielli
, Stefano A. Serapian
, Lara Mussolin, Elisabetta Moroni, Giorgio Colombo
:
Integrating Protein Interaction Surface Prediction with a Fragment-Based Drug Design: Automatic Design of New Leads with Fragments on Energy Surfaces. 343-353 - Madelyn Smith
, Pengfei Li
:
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study. 354-361 - Xiaoyue Ji, Hao Liu, Yangpeng Zhang, Jun Chen, Hai-Feng Chen
:
Personal Precise Force Field for Intrinsically Disordered and Ordered Proteins Based on Deep Learning. 362-374 - Reem A. Alkhodier, Sushil Kumar Mishra
, Robert J. Doerksen
, David A. Colby
:
Comparison of Conformational Analyses of Naturally Occurring Flavonoid-O-Glycosides with Unnatural Flavonoid-CF2-Glycosides Using Molecular Modeling. 375-386 - Marley L. Samways
, Hannah E. Bruce Macdonald
, Richard D. Taylor
, Jonathan W. Essex
:
Water Networks in Complexes between Proteins and FDA-Approved Drugs. 387-396 - Yan Liu, He Yan, Long-Chen Shen, Dong-Jun Yu
:
Learning Cell Annotation under Multiple Reference Datasets by Multisource Domain Adaptation. 397-405 - Stefano Costanzi
, Charlotte K. Slavick, Brent O. Hutcheson, Gregory D. Koblentz, Richard T. Cupitt:
Correction to "Lists of Chemical Warfare Agents and Precursors from International Nonproliferation Frameworks: Structural Annotation and Chemical Fingerprint Analysis". 406
Volume 63, Number 2, January 2023
- Diego Enry Barreto Gomes, Katia Galentino
, Marion Sisquellas, Luca Monari, Cédric Bouysset, Marco Cecchini
:
ChemFlow─From 2D Chemical Libraries to Protein-Ligand Binding Free Energies. 407-411 - Kristian Kríz
, Lisa Schmidt
, Alfred T. Andersson
, Marie-Madeleine Walz
, David van der Spoel
:
An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation. 412-431 - Raghad Al-Jarf, Simon Tang
, Douglas E. V. Pires
, David B. Ascher
:
embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules. 432-441 - Raya Stoyanova, Paul Maximilian Katzberger, Leonid Komissarov, Aous Khadhraoui, Lisa Sach-Peltason, Katrin Groebke Zbinden, Torsten Schindler, Nenad Manevski
:
Computational Predictions of Nonclinical Pharmacokinetics at the Drug Design Stage. 442-458 - Cesare Roncaglia, Riccardo Ferrando
:
Machine Learning Assisted Clustering of Nanoparticle Structures. 459-473 - Iori Azuma, Tadahaya Mizuno
, Hiroyuki Kusuhara:
NRBdMF: A Recommendation Algorithm for Predicting Drug Effects Considering Directionality. 474-483 - Ye Buehler
, Jean-Louis Reymond
:
Molecular Framework Analysis of the Generated Database GDB-13s. 484-492 - Yangcheng Ai, Zichao Yang, Zilong Yang
, Shanhe Wan, Chunhui Huang, Chuan Huang, Mingxia Li, Zhonghuang Li, Jiajie Zhang
, Tingting Zhang
:
Discovery and Computational Studies of Potent Covalent Kinase Inhibitors with α-Substituent Electrophiles Targeting Cysteine. 493-506 - Sebastián Adolfo Cuesta, Martín Moreno
, Romina A. López, José Ramón Mora
, José Luis Paz
, Edgar Márquez
:
ElectroPredictor: An Application to Predict Mayr's Electrophilicity E through Implementation of an Ensemble Model Based on Machine Learning Algorithms. 507-521 - Reecan J. Juarez, Yaoyukun Jiang
, Matthew Tremblay, Qianzhen Shao, A. James Link
, Zhongyue J. Yang
:
LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling. 522-530 - Luca Mollica
, Gabriele Giachin
:
Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study. 531-545 - Alexander Zlobin
, Julia Belyaeva, Andrey Golovin:
Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms. 546-560 - Yishui Li, Runduo Liu, Jie Liu, Haibin Luo, Chengkun Wu, Zhe Li
:
An Open Source Graph-Based Weighted Cycle Closure Method for Relative Binding Free Energy Calculations. 561-570 - Namita Dube, Sabab Hasan Khan, Riley Sasse, C. Denise Okafor
:
Identification of an Evolutionarily Conserved Allosteric Network in Steroid Receptors. 571-582 - Filipp Gusev
, Evgeny Gutkin
, Maria Kurnikova
, Olexandr Isayev
:
Active Learning Guided Drug Design Lead Optimization Based on Relative Binding Free Energy Modeling. 583-594 - Federico N. Pedron
, Andresa Messias
, Ari Zeida
, Adrian E. Roitberg
, Dario A. Estrin
:
Novel Lennard-Jones Parameters for Cysteine and Selenocysteine in the AMBER Force Field. 595-604 - Xiaokun Hong, Kaiyuan Song, Mueed Ur Rahman, Ting Wei, Yan Zhang
, Lin-Tai Da
, Hai-Feng Chen
:
Phosphorylation Regulation Mechanism of β2 Integrin for the Binding of Filamin Revealed by Markov State Model. 605-618 - Jie Gao
, Yaoliang Zhang
, Lin Yu, Yuejuan Li
, Shumin Liao, Jian Wang
, Lijie Guan
:
Identification of Enolase 1 as a Potential Target for Magnaporthe oryzae: Integrated Proteomic and Molecular Dynamics Simulation. 619-632 - Natasha Gupta Vergara, Megan Gatchel, Cameron F. Abrams
:
Entropic Overcompensation of the N501Y Mutation on SARS-CoV-2 S Binding to ACE2. 633-642 - Ke Zuo, Riccardo Capelli
, Giulia Rossetti
, Rachel Nechushtai
, Paolo Carloni
:
Predictions of the Poses and Affinity of a Ligand over the Entire Surface of a NEET Protein: The Case of Human MitoNEET. 643-654 - Zakir Ali
, Ambika Goyal, Ayush Jhunjhunwala, Abhijit Mitra
, John F. Trant
, Purshotam Sharma
:
Structural and Energetic Features of Base-Base Stacking Contacts in RNA. 655-669 - Rojalin Pradhan, Sibarama Panigrahi
, Prabhat K. Sahu
:
Conformational Search for the Building Block of Proteins Based on the Gradient Gravitational Search Algorithm (ConfGGS) Using Force Fields: CHARMM, AMBER, and OPLS-AA. 670-690
Volume 63, Number 3, February 2023
- Fabio Urbina, Filippa Lentzos, Cédric Invernizzi
, Sean Ekins
:
Preventing AI From Creating Biochemical Threats. 691-694 - Yan A. Ivanenkov
, Daniil Polykovskiy
, Dmitry Bezrukov, Bogdan Zagribelnyy, Vladimir Aladinskiy, Petrina Kamya, Alex Aliper, Feng Ren
, Alex Zhavoronkov
:
Chemistry42: An AI-Driven Platform for Molecular Design and Optimization. 695-701 - Cécile Hilpert
, Louis Beranger
, Paulo Cesar Telles de Souza
, Petteri A. Vainikka
, Vincent Nieto
, Siewert J. Marrink
, Luca Monticelli
, Guillaume Launay
:
Facilitating CG Simulations with MAD: The MArtini Database Server. 702-710 - Madushanka Manathunga
, Hasan Metin Aktulga, Andreas W. Götz
, Kenneth M. Merz Jr.
:
Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units. 711-717 - Mateusz K. Bieniek
, Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan
, Peter V. Coveney
:
TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal. 718-724 - Adem R. N. Aouichaoui
, Fan Fan, Seyed Soheil Mansouri
, Jens Abildskov
, Gürkan Sin
:
Combining Group-Contribution Concept and Graph Neural Networks Toward Interpretable Molecular Property Models. 725-744 - Lincan Fang, Xiaomi Guo, Milica Todorovic
, Patrick Rinke
, Xi Chen
:
Exploring the Conformers of an Organic Molecule on a Metal Cluster with Bayesian Optimization. 745-752 - Frank W. Marrs
, Jack V. Davis, Alexandra C. Burch, Geoffrey W. Brown, Nicholas Lease
, Patricia L. Huestis, Marc J. Cawkwell
, Virginia W. Manner
:
Chemical Descriptors for a Large-Scale Study on Drop-Weight Impact Sensitivity of High Explosives. 753-769 - Yixiang Ruan, Sen Lin, Yiming Mo
:
AROPS: A Framework of Automated Reaction Optimization with Parallelized Scheduling. 770-781 - Donghan Wang
, Wenze Li, Xu Dong, Hongzhi Li, Lihong Hu
:
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion. 782-793 - Kohei Nemoto, Hiromasa Kaneko
:
De Novo Direct Inverse QSPR/QSAR: Chemical Variational Autoencoder and Gaussian Mixture Regression Models. 794-805 - Yufeng Liu
, Zhenyu Li
:
Predict Ionization Energy of Molecules Using Conventional and Graph-Based Machine Learning Models. 806-814 - Yuqing Yang, Dongping Liu, Zhendong Hua, Peng Xu, Youmei Wang, Bin Di
, Jun Liao, Mengxiang Su
:
Machine Learning-Assisted Rapid Screening of Four Types of New Psychoactive Substances in Drug Seizures. 815-825 - Adnan Khan, Jamal Uddin, Farman Ali
, Harish Kumar, Wajdi Alghamdi, Aftab Ahmad:
AFP-SPTS: An Accurate Prediction of Antifreeze Proteins Using Sequential and Pseudo-Tri-Slicing Evolutionary Features with an Extremely Randomized Tree. 826-834 - Haiping Zhang
, Konda Mani Saravanan
, Yanjie Wei, Yang Jiao, Yang Yang, Yi Pan, Xuli Wu, John Z. H. Zhang:
Deep Learning-Based Bioactive Therapeutic Peptide Generation and Screening. 835-845 - Tuan Xu, Md Kabir, Srilatha Sakamuru
, Pranav Shah, Elias C. Padilha, Deborah K. Ngan, Menghang Xia
, Xin Xu, Anton Simeonov, Ruili Huang
:
Predictive Models for Human Cytochrome P450 3A7 Selective Inhibitors and Substrates. 846-855 - Seungchan An
, Seok Young Hwang, Junpyo Gong, Sungjin Ahn
, In Guk Park, Soyeon Oh, Young-Won Chin
, Minsoo Noh
:
Computational Prediction of the Phenotypic Effect of Flavonoids on Adiponectin Biosynthesis. 856-869 - Sneha Thomas, Kevin S. Silmore
, Piyush Sharma, Ananth Govind Rajan
:
Enumerating Stable Nanopores in Graphene and Their Geometrical Properties Using the Combinatorics of Hexagonal Lattices. 870-881 - Álvaro Pérez-Barcia, Gustavo Cárdenas, Juan J. Nogueira
, Marcos Mandado
:
Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis. 882-897 - Francesca Peccati
, Sara Alunno-Rufini
, Gonzalo Jiménez-Osés
:
Accurate Prediction of Enzyme Thermostabilization with Rosetta Using AlphaFold Ensembles. 898-909 - Abhishek Acharya
, Ishan Ghai, Claudio Piselli
, Jigneshkumar Dahyabhai Prajapati
, Roland Benz
, Mathias Winterhalter
, Ulrich Kleinekathöfer
:
Conformational Dynamics of Loop L3 in OmpF: Implications toward Antibiotic Translocation and Voltage Gating. 910-927 - Efpraxia Tzortzini, Robin A. Corey
, Antonios Kolocouris
:
Comparative Study of Receptor-, Receptor State-, and Membrane-Dependent Cholesterol Binding Sites in A2A and A1 Adenosine Receptors Using Coarse-Grained Molecular Dynamics Simulations. 928-949 - Santiago Movilla
, Sergio Martí
, Maite Roca
, Vicent Moliner
:
Computational Study of the Inhibition of RgpB Gingipain, a Promising Target for the Treatment of Alzheimer's Disease. 950-958 - Krishna Prasad Ghanta, Souvik Mondal, Timir Hajari
, Sanjoy Bandyopadhyay
:
Impact of an Ionic Liquid on Amino Acid Side Chains: A Perspective from Molecular Simulation Studies. 959-972 - Patrice Koehl
, Arseniy V. Akopyan, Herbert Edelsbrunner:
Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives. 973-985 - Yazdan Maghsoud
, Erik Antonio Vázquez-Montelongo
, Xudong Yang, Chengwen Liu
, Zhifeng Jing
, Juhoon Lee, Matthew Harger, Ally K. Smith, Miguel Espinoza, Hou-Fu Guo, Jonathan M. Kurie, Kevin N. Dalby
, Pengyu Y. Ren
, G. Andrés Cisneros
:
Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. 986-1001 - Saikat Pal
, Amit Kumar, Harish Vashisth
:
Role of Dynamics and Mutations in Interactions of a Zinc Finger Antiviral Protein with CG-rich Viral RNA. 1002-1011 - Adam Stasiulewicz
, Anna Lesniak, Magdalena Bujalska-Zadrozny, Tomasz Pawinski, Joanna I. Sulkowska
:
Identification of Novel CB2 Ligands through Virtual Screening and In Vitro Evaluation. 1012-1027 - Horrick Sharma, Pragya Sharma, Uzziah Urquiza, Lerin R. Chastain, Michael A. Ihnat:
Exploration of a Large Virtual Chemical Space: Identification of Potent Inhibitors of Lactate Dehydrogenase-A against Pancreatic Cancer. 1028-1043 - Jun Hu
, Wen-Wu Zeng, Ning-Xin Jia, Muhammad Arif, Dong-Jun Yu
, Gui-Jun Zhang:
Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm. 1044-1057 - Kai Kang
, Lei Wang
, Chen Song
:
ProtRAP: Predicting Lipid Accessibility Together with Solvent Accessibility of Proteins in One Run. 1058-1065 - Ran Liu, Xiang Liu
, Jie Wu:
Persistent Path-Spectral (PPS) Based Machine Learning for Protein-Ligand Binding Affinity Prediction. 1066-1075 - Xue-Qiang Fan, Bing Lin, Jun Hu, Zhong-Yi Guo
:
I-DNAN6mA: Accurate Identification of DNA N6-Methyladenine Sites Using the Base-Pairing Map and Deep Learning. 1076-1086
Volume 63, Number 4, February 2023
- Darya Stepanenko, Stephanie Budhan, Carlos Simmerling
:
SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein. 1087-1092 - Jan-Oliver Felix Kapp-Joswig
, Bettina G. Keller:
CommonNNClustering─A Python Package for Generic Common-Nearest-Neighbor Clustering. 1093-1098 - Jonathan G. M. Conn, James W. Carter, Justin J. A. Conn, Vigneshwari Subramanian
, Andrew Baxter, Ola Engkvist
, Antonio Llinàs
, Ekaterina Ratkova, Stephen D. Pickett
, James L. McDonagh
, David S. Palmer
:
Blinded Predictions and Post Hoc Analysis of the Second Solubility Challenge Data: Exploring Training Data and Feature Set Selection for Machine and Deep Learning Models. 1099-1113 - Mohammadamin Tavakoli, Yin Ting T. Chiu
, Pierre Baldi
, Ann Marie Carlton
, David Van Vranken
:
RMechDB: A Public Database of Elementary Radical Reaction Steps. 1114-1123 - Sergei A. Evteev
, Alexey V. Ereshchenko, Yan A. Ivanenkov:
SiteRadar: Utilizing Graph Machine Learning for Precise Mapping of Protein-Ligand-Binding Sites. 1124-1132 - Jintu Zhang
, Haotian Zhang, Zhixin Qin, Yu Kang
, Xin Hong
, Tingjun Hou
:
Quasiclassical Trajectory Simulation as a Protocol to Build Locally Accurate Machine Learning Potentials. 1133-1142 - Jiali Guo, Ming Sun, Xueyan Zhao, Chaojie Shi, Haoming Su, Yanzhi Guo, Xuemei Pu
:
General Graph Neural Network-Based Model To Accurately Predict Cocrystal Density and Insight from Data Quality and Feature Representation. 1143-1156 - José Manuel Vásquez-Pérez
, Luis Ángel Zárate-Hernández
, Carlos Zepactonal Gómez-Castro
, Uriel Alejandro Nolasco-Hernández:
A Practical Algorithm to Solve the Near-Congruence Problem for Rigid Molecules and Clusters. 1157-1165 - Benjamin I. Tingle, Khanh G. Tang, Mar Castanon, John J. Gutierrez, Munkhzul Khurelbaatar, Chinzorig Dandarchuluun, Yurii S. Moroz, John J. Irwin
:
ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery. 1166-1176 - Mengxian Yu, Yajuan Shi, Qingzhu Jia, Qiang Wang, Zheng-Hong Luo
, Fangyou Yan
, Yin-Ning Zhou
:
Ring Repeating Unit: An Upgraded Structure Representation of Linear Condensation Polymers for Property Prediction. 1177-1187 - Bumjoon Seo
, Brett M. Savoie
:
Evidence That Less Can Be More for Transferable Force Fields. 1188-1195 - Zoe Li
, Kevin C. Chan
, Jonathan D. Nickels
, Xiaolin Cheng
:
Molecular Dynamics Refinement of Open State Serotonin 5-HT3A Receptor Structures. 1196-1207 - Sara Gómez
, Piero Lafiosca
, Franco Egidi
, Tommaso Giovannini
, Chiara Cappelli
:
UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA. 1208-1217 - Brad Crawford
, Umesh Timalsina, Co D. Quach, Nicholas C. Craven, Justin B. Gilmer, Clare McCabe
, Peter T. Cummings, Jeffrey J. Potoff
:
MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC. 1218-1228