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ORCIDJournal of Chemical Information and Modeling, Volume 61
Volume 61, Number 1, January 2021
- Issue Publication Information.
- Issue Editorial Masthead.
- Junyong Lai
, Xiangbin Li, Yanxing Wang, Shiqiu Yin, Jielong Zhou, Zhenming Liu:
AIScaffold: A Web-Based Tool for Scaffold Diversification Using Deep Learning. 1-6 - Maria Korshunova, Boris Ginsburg, Alexander Tropsha, Olexandr Isayev:
OpenChem: A Deep Learning Toolkit for Computational Chemistry and Drug Design. 7-13 - Feng-Xu Wu, Jing-Fang Yang, Long-Can Mei, Fan Wang, Ge-Fei Hao, Guangfu Yang:
PIIMS Server: A Web Server for Mutation Hotspot Scanning at the Protein-Protein Interface. 14-20 - Wenqiang Jia, Zhuo Yang, Minjian Yang, Liang Cheng, Zengrong Lei, Xiaojian Wang:
Machine Learning Enhanced Spectrum Recognition Based on Computer Vision (SRCV) for Intelligent NMR Data Extraction. 21-25 - Edgar López-López, Jürgen Bajorath, José L. Medina-Franco:
Informatics for Chemistry, Biology, and Biomedical Sciences. 26-35 - Minsup Kim, Kichul Park, Wonsang Kim, Sangwon Jung, Art E. Cho:
Target-Specific Drug Design Method Combining Deep Learning and Water Pharmacophore. 36-45 - Mostafa Karimi, Di Wu, Zhangyang Wang, Yang Shen:
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts. 46-66 - Rafael Mamede, Bruno Simões de-Almeida, Mengyao Chen, Qing-You Zhang, João Aires-de-Sousa:
Machine Learning Classification of One-Chiral-Center Organic Molecules According to Optical Rotation. 67-75 - Aurelio Antelo-Collado, Ramón Carrasco-Velar, Nicolás García-Pedrajas, Gonzalo Cerruela García:
Effective Feature Selection Method for Class-Imbalance Datasets Applied to Chemical Toxicity Prediction. 76-94 - Rainier Barrett, Andrew D. White:
Investigating Active Learning and Meta-Learning for Iterative Peptide Design. 95-105 - Abhishek Aggarwal, Vinayak Vinayak, Saientan Bag, Chiranjib Bhattacharyya, Umesh V. Waghmare, Prabal K. Maiti:
Predicting the DNA Conductance Using a Deep Feedforward Neural Network Model. 106-114 - Derek P. Metcalf, Andy Jiang, Steven A. Spronk, Daniel L. Cheney, C. David Sherrill:
Electron-Passing Neural Networks for Atomic Charge Prediction in Systems with Arbitrary Molecular Charge. 115-122 - Eunji Kim, Dongseon Lee, Youngchun Kwon, Min Sik Park, Youn-Suk Choi:
Valid, Plausible, and Diverse Retrosynthesis Using Tied Two-Way Transformers with Latent Variables. 123-133 - Joydeep Munshi, Wei Chen, TeYu Chien, Ganesh Balasubramanian:
Transfer Learned Designer Polymers For Organic Solar Cells. 134-142 - Thomas Specht, Kerstin Münnemann, Hans Hasse, Fabian Jirasek:
Automated Methods for Identification and Quantification of Structural Groups from Nuclear Magnetic Resonance Spectra Using Support Vector Classification. 143-155 - Michael R. Maser, Alexander Y. Cui, Serim Ryou, Travis J. DeLano, Yisong Yue, Sarah E. Reisman:
Multilabel Classification Models for the Prediction of Cross-Coupling Reaction Conditions. 156-166 - Robert Schmidt, Florian Krull, Anna Lina Heinzke, Matthias Rarey:
Disconnected Maximum Common Substructures under Constraints. 167-178 - Yuliana Zabolotna, Arkadii I. Lin, Dragos Horvath, Gilles Marcou, Dmitriy M. Volochnyuk, Alexandre Varnek:
Chemography: Searching for Hidden Treasures. 179-188 - Jeffrey L. Mendenhall, Benjamin P. Brown, Sandeepkumar Kothiwale, Jens Meiler:
BCL: : Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database. 189-201 - Shweta Singh Chauhan, Deepak Kumar Sachan, Ramakrishnan Parthasarathi:
FOCUS-DB: An Online Comprehensive Database on Food Additive Safety. 202-210 - Ben Joseph R. Cuyacot, Ivo Durník, Cina Foroutan-Nejad, Radek Marek:
Anatomy of Base Pairing in DNA by Interacting Quantum Atoms. 211-222 - Natalia Díaz, Dimas Suárez:
Understanding the Conformational Properties of Fluorinated Polypeptides: Molecular Modelling of Unguisin A. 223-237 - Louis Bellmann, Patrick Penner, Matthias Rarey:
Topological Similarity Search in Large Combinatorial Fragment Spaces. 238-251 - Rong Yang, Zhenxing Chen, Fuda Xie, Mingxiang Xie, Na Liu, Ziren Su, Jiangyong Gu, Ruizhi Zhao:
(+/-)-Borneol Reverses Mitoxantrone Resistance against P-Glycoprotein. 252-262 - Flaviu S. Cipcigan, Paul Smith, Jason Crain, Anders Hogner, Leonardo De Maria, Antonio Llinàs, Ekaterina Ratkova:
Membrane Permeability in Cyclic Peptides is Modulated by Core Conformations. 263-269 - Guglielmo Monaco, Francesco Ferdinando Summa, Riccardo Zanasi:
Program Package for the Calculation of Origin-Independent Electron Current Density and Derived Magnetic Properties in Molecular Systems. 270-283 - Zhe Huai, Zhaoxi Shen, Zhaoxi Sun:
Binding Thermodynamics and Interaction Patterns of Inhibitor-Major Urinary Protein-I Binding from Extensive Free-Energy Calculations: Benchmarking AMBER Force Fields. 284-297 - Leena Aggarwal, Parbati Biswas:
Hydration Thermodynamics of the N-Terminal FAD Mutants of Amyloid-β. 298-310 - José-Emilio Sánchez-Aparicio, Laura Tiessler-Sala, Lorea Velasco-Carneros, Lorena Roldán-Martín, Giuseppe Sciortino, Jean-Didier Maréchal:
BioMetAll: Identifying Metal-Binding Sites in Proteins from Backbone Preorganization. 311-323 - Neda Ojaghlou, Justin Airas, Lauren M. McRae, Cooper A. Taylor, Bill R. Miller, Carol A. Parish:
Understanding the Structure and Apo Dynamics of the Functionally Active JIP1 Fragment. 324-334 - Filipe M. Sousa, Luís M. P. Lima, Clément Arnarez, Manuela M. Pereira, Manuel N. Melo:
Coarse-Grained Parameterization of Nucleotide Cofactors and Metabolites: Protonation Constants, Partition Coefficients, and Model Topologies. 335-346 - Tandac F. Guclu, Nazli Kocatug, Ali Rana Atilgan, Canan Atilgan:
N-Terminus of the Third PDZ Domain of PSD-95 Orchestrates Allosteric Communication for Selective Ligand Binding. 347-357 - Lovika Mittal, Mitul Srivastava, Anita Kumari, Rajiv K. Tonk, Amit Awasthi, Shailendra Asthana:
Interplay among Structural Stability, Plasticity, and Energetics Determined by Conformational Attuning of Flexible Loops in PD-1. 358-384 - Anastasia G. Konshina, Peter V. Dubovskii, Roman G. Efremov:
Stepwise Insertion of Cobra Cardiotoxin CT2 into a Lipid Bilayer Occurs as an Interplay of Protein and Membrane "Dynamic Molecular Portraits". 385-399 - Shuhua Ma, Jack A. Henderson, Jana Shen:
Exploring the pH-Dependent Structure-Dynamics-Function Relationship of Human Renin. 400-407 - Martín Soñora, Leandro Martínez, Sergio Pantano, Matías R. Machado:
Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus. 408-422 - Subhomoi Borkotoky, Debajit Dey, Manidipa Banerjee:
Computational Insight Into the Mechanism of SARS-CoV-2 Membrane Fusion. 423-431 - Karnesh Jain, Othman Ghribi, Jerome Delhommelle:
Folding Free-Energy Landscape of α-Synuclein (35-97) Via Replica Exchange Molecular Dynamics. 432-443 - Biswajit Gorai, Anil Kumar Sahoo, Anand Srivastava, Narendra M. Dixit, Prabal K. Maiti:
Concerted Interactions between Multiple gp41 Trimers and the Target Cell Lipidome May Be Required for HIV-1 Entry. 444-454 - Krzysztof K. Bojarski, Sergey A. Samsonov:
Role of Oligosaccharide Chain Polarity in Protein-Glycosaminoglycan Interactions. 455-466 - Horacio Pérez Sánchez, Helena den-Haan, Alfonso Pérez-Garrido, Jorge Peña-García, Sandipan Chakraborty, Ilkay Erdogan Orhan, Fatma Sezer Senol Deniz, José Manuel Villalgordo:
Combined Structure and Ligand-Based Design of Selective Acetylcholinesterase Inhibitors. 467-480 - Katherine J. Schultz, Sean M. Colby, Vivian S. Lin, Aaron T. Wright, Ryan S. Renslow:
Ligand- and Structure-Based Analysis of Deep Learning-Generated Potential α2a Adrenoceptor Agonists. 481-492 - Hanyu Gao, Jean Pauphilet, Thomas J. Struble, Connor W. Coley, Klavs F. Jensen:
Direct Optimization across Computer-Generated Reaction Networks Balances Materials Use and Feasibility of Synthesis Plans for Molecule Libraries. 493-504 - Jun Hu, Liang Rao, Yi-Heng Zhu, Gui-Jun Zhang, Dong-Jun Yu:
TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features. 505-515 - Ju Zhang, Jialin Yu, Dan Lin, Xinyun Guo, Huan He, Shaoping Shi:
DeepCLA: A Hybrid Deep Learning Approach for the Identification of Clathrin. 516-524 - Ruyu Dai, Wei Zhang, Wending Tang, Evelien Wynendaele, Qizhi Zhu, Yannan Bin, Bart De Spiegeleer, Junfeng Xia:
BBPpred: Sequence-Based Prediction of Blood-Brain Barrier Peptides with Feature Representation Learning and Logistic Regression. 525-534 - Hugo Guterres, Sang-Jun Park, Wei Jiang, Wonpil Im:
Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures. 535-546
Volume 61, Number 2, February 2021
- Issue Editorial Masthead.
- Issue Publication Information.
- Guo-Wei Wei, Thereza A. Soares, Habibah A. Wahab, Renxiao Wang:
Computational Chemistry in Asia. 547 - Daniel Mulnaes, Filip Koenig, Holger Gohlke:
TopSuite Web Server: A Meta-Suite for Deep-Learning-Based Protein Structure and Quality Prediction. 548-553 - Timur Gimadiev, Ramil I. Nugmanov, Dinar Batyrshin, Timur I. Madzhidov, Satoshi Maeda, Pavel Sidorov, Alexandre Varnek:
Combined Graph/Relational Database Management System for Calculated Chemical Reaction Pathway Data. 554-559 - Benjamin Ries, Stephanie M. Linker, David F. Hahn, Gerhard König, Sereina Riniker:
Ensembler: A Simple Package for Fast Prototyping and Teaching Molecular Simulations. 560-564 - Charles N. Lowe, Antony J. Williams:
Enabling High-Throughput Searches for Multiple Chemical Data Using the U.S.-EPA CompTox Chemicals Dashboard. 565-570 - Aamir Mehmood, Aman Chandra Kaushik, Qiankun Wang, Cheng-Dong Li, Dong-Qing Wei:
Bringing Structural Implications and Deep Learning-Based Drug Identification for KRAS Mutants. 571-586 - Kevin McLoughlin, Claire G. Jeong, Thomas D. Sweitzer, Amanda J. Minnich, Margaret Tse, Brian J. Bennion, Jonathan E. Allen, Stacie Calad-Thomson, Tom Rush, Jim Brase:
Machine Learning Models to Predict Inhibition of the Bile Salt Export Pump. 587-602 - Benjamin P. Brown, Jeffrey L. Mendenhall, Alexander R. Geanes, Jens Meiler:
General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps. 603-620 - Sowmya Ramaswamy Krishnan, Navneet Bung, Gopalakrishnan Bulusu, Arijit Roy:
Accelerating De Novo Drug Design against Novel Proteins Using Deep Learning. 621-630 - Andrei Buin, Hung Yi Chiang, S. Andrew Gadsden, Faraz A. Alderson:
Permutationally Invariant Deep Learning Approach to Molecular Fingerprinting with Application to Compound Mixtures. 631-640 - Haris Hasic, Takashi Ishida:
Single-Step Retrosynthesis Prediction Based on the Identification of Potential Disconnection Sites Using Molecular Substructure Fingerprints. 641-652 - Sankalp Jain, Vishal B. Siramshetty, Vinicius M. Alves, Eugene N. Muratov, Nicole C. Kleinstreuer, Alexander Tropsha, Marc C. Nicklaus, Anton Simeonov, Alexey V. Zakharov:
Large-Scale Modeling of Multispecies Acute Toxicity End Points Using Consensus of Multitask Deep Learning Methods. 653-663 - Janosch Menke, Oliver Koch:
Using Domain-Specific Fingerprints Generated Through Neural Networks to Enhance Ligand-Based Virtual Screening. 664-675 - Anju Sharma, Rajnish Kumar, Shabnam Ranjta, Pritish Kumar Varadwaj:
SMILES to Smell: Decoding the Structure-Odor Relationship of Chemical Compounds Using the Deep Neural Network Approach. 676-688 - Yashaswi Pathak, Sarvesh Mehta, U. Deva Priyakumar:
Learning Atomic Interactions through Solvation Free Energy Prediction Using Graph Neural Networks. 689-698 - Reed M. Stein, Ying Yang, Trent E. Balius, Matt J. O'Meara, Jiankun Lyu, Jennifer Young, Khanh G. Tang, Brian K. Shoichet, John J. Irwin:
Property-Unmatched Decoys in Docking Benchmarks. 699-714 - Aida Shahraki, Ali Isbilir, Berna Dogan, Martin J. Lohse, Serdar Durdagi, Necla Birgul-Iyison:
Structural and Functional Characterization of Allatostatin Receptor Type-C of Thaumetopoea pityocampa, a Potential Target for Next-Generation Pest Control Agents. 715-728 - Mahendra Awale, Jérôme Hert, Laura Guasch, Sereina Riniker, Christian Kramer:
The Playbooks of Medicinal Chemistry Design Moves. 729-742 - Lucian Chan, Geoffrey R. Hutchison, Garrett M. Morris:
Understanding Ring Puckering in Small Molecules and Cyclic Peptides. 743-755 - Matevz Pesek, Andraz Juvan, Jure Jakos, Janez Kosmrlj, Matija Marolt, Martin Gazvoda:
Database Independent Automated Structure Elucidation of Organic Molecules Based on IR, 1H NMR, 13C NMR, and MS Data. 756-763 - Qiaoyu Hu, Vindi M. Jayasinghe-Arachchige, Rajeev Prabhakar:
Degradation of a Main Plastic Pollutant Polyethylene Terephthalate by Two Distinct Proteases (Neprilysin and Cutinase-like Enzyme). 764-776 - Daisuke Takaya, Chiduru Watanabe, Shunpei Nagase, Kikuko Kamisaka, Yoshio Okiyama, Hirotomo Moriwaki, Hitomi Yuki, Tomohiro Sato, Noriyuki Kurita, Yoichiro Yagi, Tatsuya Takagi, Norihito Kawashita, Kenichiro Takaba, Tomonaga Ozawa, Midori Takimoto-Kamimura, Shigenori Tanaka, Kaori Fukuzawa, Teruki Honma:
FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method. 777-794 - Erna K. Wieduwilt, Jean-Charles Boisson, Giancarlo Terraneo, Eric Hénon, Alessandro Genoni:
A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach. 795-809 - Steven W. Rick, Gregory J. Schwing, Christopher M. Summa:
An Implementation of Replica Exchange with Dynamical Scaling for Efficient Large-Scale Simulations. 810-818 - Ivo Kabelka, Radim Brozek, Robert Vácha:
Selecting Collective Variables and Free-Energy Methods for Peptide Translocation across Membranes. 819-830 - Ya Gao, Jumin Lee, Iain Peter Shand Smith, Hwayoung Lee, Seonghoon Kim, Yifei Qi, Jeffery B. Klauda, Göran Widmalm, Syma Khalid, Wonpil Im:
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides. 831-839 - Vilde Bråten, Øivind Wilhelmsen, Sondre Kvalvåg Schnell:
Chemical Potential Differences in the Macroscopic Limit from Fluctuations in Small Systems. 840-855 - Shiji Zhao, Andrew J. Schaub, Shiou-Chuan Tsai, Ray Luo:
Development of a Pantetheine Force Field Library for Molecular Modeling. 856-868 - Arkajyoti Sengupta, Zhen Li, Lin Frank Song, Pengfei Li, Kenneth M. Merz Jr.:
Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. 869-880 - Yuemei Li, Rui Wang, Yongmei Li, Wei Zheng:
First-Principles Calculation of Photoelectric Property in Upconversion Materials through In3+ Doping. 881-890 - Maohua Yang, Yegen Tang, Jingwei Weng, Zhijun Liu, Wenning Wang:
The Role of Calcium in Regulating the Conformational Dynamics of d-Galactose/d-Glucose-Binding Protein Revealed by Markov State Model Analysis. 891-900 - Davide Sala, Andrea Giachetti, Antonio Rosato:
Insights into the Dynamics of the Human Zinc Transporter ZnT8 by MD Simulations. 901-912 - Javier Rodríguez-Salarichs, Mario García de Lacoba, Alicia Prieto, María Jesús Martínez, Jorge Barriuso:
Versatile Lipases from the Candida rugosa-like Family: A Mechanistic Insight Using Computational Approaches. 913-920 - Weikang Gong, Yang Liu, Yanpeng Zhao, Shihao Wang, Zhongjie Han, Chunhua Li:
Equally Weighted Multiscale Elastic Network Model and Its Comparison with Traditional and Parameter-Free Models. 921-937 - Hanne S. Antila, Tiago M. Ferreira, Samuli Ollila, Markus Miettinen:
Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics. 938-949 - Dizhou Wu, Jiajie Xiao, Freddie R. Salsbury Jr.:
Light Chain Mutation Effects on the Dynamics of Thrombin. 950-965 - Yunxiang Sun, Junchao Huang, Xiangmei Duan, Feng Ding:
Direct Observation of β-Barrel Intermediates in the Self-Assembly of Toxic SOD128-38 and Absence in Nontoxic Glycine Mutants. 966-975 - Lucy Kate Ladefoged, Birgit Schiøtt, Natalya U. Fedosova:
Beneficent and Maleficent Effects of Cations on Bufadienolide Binding to Na+, K+-ATPase. 976-986 - Mayk C. Ramos, Bruno A. C. Horta:
Drug-Loading Capacity of PAMAM Dendrimers Encapsulating Quercetin Molecules: A Molecular Dynamics Study with the 2016H66 Force Field. 987-1000 - André Fischer, Florian Häuptli, Markus A. Lill, Martin Smiesko:
Computational Assessment of Combination Therapy of Androgen Receptor-Targeting Compounds. 1001-1009 - André Fischer, Gabriela Frehner, Markus A. Lill, Martin Smiesko:
Conformational Changes of Thyroid Receptors in Response to Antagonists. 1010-1019 - Anjela Manandhar, Benjamin E. Blass, Dennis J. Colussi, Imane Almi, Magid Abou-Gharbia, Michael L. Klein, Khaled M. Elokely:
Targeting SARS-CoV-2 M3CLpro by HCV NS3/4a Inhibitors: In Silico Modeling and In Vitro Screening. 1020-1032
Volume 61, Number 3, March 2021
- Issue Editorial Masthead.
- Issue Publication Information.
- Tesia M. Bobrowski, Daniel Robert Korn, Eugene N. Muratov, Alexander Tropsha:
ZINC Express: A Virtual Assistant for Purchasing Compounds Annotated in the ZINC Database. 1033-1036 - Junxi Mu, Hao Liu, Jian Zhang, Ray Luo, Hai-Feng Chen:
Recent Force Field Strategies for Intrinsically Disordered Proteins. 1037-1047 - Yunhui Ge, David F. Hahn, David L. Mobley:
A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations. 1048-1052 - Cheng-Wei Ju, Hanzhi Bai, Bo Li, Rizhang Liu:
Machine Learning Enables Highly Accurate Predictions of Photophysical Properties of Organic Fluorescent Materials: Emission Wavelengths and Quantum Yields. 1053-1065 - Ziteng Liu, Liqiang Lin, Qingqing Jia, Zheng Cheng, Yanyan Jiang, Yanwen Guo, Jing Ma:
Transferable Multilevel Attention Neural Network for Accurate Prediction of Quantum Chemistry Properties via Multitask Learning. 1066-1082 - José Jiménez-Luna, Miha Skalic, Nils Weskamp, Gisbert Schneider:
Coloring Molecules with Explainable Artificial Intelligence for Preclinical Relevance Assessment. 1083-1094 - Jianing Lu, Song Xia, Jieyu Lu, Yingkai Zhang:
Dataset Construction to Explore Chemical Space with 3D Geometry and Deep Learning. 1095-1104 - Mrityunjay Singh, Mitul Srivastava, Sharad R. Wakode, Shailendra Asthana:
Elucidation of Structural Determinants Delineates the Residues Playing Key Roles in Differential Dynamics and Selective Inhibition of Sirt1-3. 1105-1124 - Johnatan Mucelini, Marcos G. Quiles, Ronaldo C. Prati, Juarez L. F. Da Silva:
Correlation-Based Framework for Extraction of Insights from Quantum Chemistry Databases: Applications for Nanoclusters. 1125-1135 - Batuhan Yildirim, Jacqueline M. Cole:
Bayesian Particle Instance Segmentation for Electron Microscopy Image Quantification. 1136-1149 - Tzyy-Shyang Lin, Nathan J. Rebello, Haley K. Beech, Zi Wang, Bassil El-Zaatari, David J. Lundberg, Jeremiah A. Johnson, Julia A. Kalow, Stephen L. Craig, Bradley D. Olsen:
PolyDAT: A Generic Data Schema for Polymer Characterization. 1150-1163 - Anastasios Gotzias:
Binding Free Energy Calculations of Bilayer Graphenes Using Molecular Dynamics. 1164-1171 - Kohei Sasaki, Takefumi Yamashita:
Modification and Validation of the DREIDING Force Field for Molecular Liquid Simulations (DREIDING-UT). 1172-1179