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ORCIDJournal of Chemical Information and Modeling, Volume 58
Volume 58, Number 1, January 2018
- Daniel Probst
, Jean-Louis Reymond:
SmilesDrawer: Parsing and Drawing SMILES-Encoded Molecular Structures Using Client-Side JavaScript. 1-7 - Sergey Ivanov, Alexey Lagunin, Anastasia V. Rudik, Dmitry Filimonov, Vladimir Poroikov:
ADVERPred-Web Service for Prediction of Adverse Effects of Drugs. 8-11 - Didier Mathieu:
Atom Pair Contribution Method: Fast and General Procedure To Predict Molecular Formation Enthalpies. 12-26 - Sabrina Jaeger, Simone Fulle, Samo Turk:
Mol2vec: Unsupervised Machine Learning Approach with Chemical Intuition. 27-35 - Yue Kong, Andreas Bender, Aixia Yan:
Identification of Novel Aurora Kinase A (AURKA) Inhibitors via Hierarchical Ligand-Based Virtual Screening. 36-47 - Ondrej Gutten, Daniel Bím, Jan Rezác, Lubomír Rulísek:
Macrocycle Conformational Sampling by DFT-D3/COSMO-RS Methodology. 48-60 - Suzanne McAnanama-Brereton, Mark P. Waller:
Rational Density Functional Selection Using Game Theory. 61-67 - Devawati Dutta, Ranjita Das, Chhabinath Mandal, Chitra Mandal:
Structure-Based Kinase Profiling To Understand the Polypharmacological Behavior of Therapeutic Molecules. 68-89 - Antoine Marion, Jerzy Góra, Oliver Kracker, Tanja Fröhr, Rafal Latajka, Norbert Sewald, Iris Antes:
Amber-Compatible Parametrization Procedure for Peptide-like Compounds: Application to 1, 4- and 1, 5-Substituted Triazole-Based Peptidomimetics. 90-110 - Mark A. Olson:
Parallel Tempering of Dark Matter from the Ebola Virus Proteome: Comparison of CHARMM36m and CHARMM22 Force Fields with Implicit Solvent. 111-118 - Hossam M. Ashtawy, Nihar R. Mahapatra:
Task-Specific Scoring Functions for Predicting Ligand Binding Poses and Affinity and for Screening Enrichment. 119-133 - Hossam M. Ashtawy, Nihar R. Mahapatra:
Descriptor Data Bank (DDB): A Cloud Platform for Multiperspective Modeling of Protein-Ligand Interactions. 134-147 - John J. Irwin, Garrett Gaskins, Teague Sterling, Michael M. Mysinger, Michael J. Keiser:
Predicted Biological Activity of Purchasable Chemical Space. 148-164 - Jan Dreher, Josef Scheiber, Nikolaus Stiefl, Knut Baumann:
xMaP - An Interpretable Alignment-Free Four-Dimensional Quantitative Structure-Activity Relationship Technique Based on Molecular Surface Properties and Conformer Ensembles. 165-181 - Kh. Dhanachandra Singh, Hamiyet Unal, Russell Desnoyer, Sadashiva S. Karnik:
Divergent Spatiotemporal Interaction of Angiotensin Receptor Blocking Drugs with Angiotensin Type 1 Receptor. 182-193 - Zhaomin Liu, Stephen J. Barigye, Moeed Shahamat, Paul Labute, Nicolas Moitessier:
Atom Types Independent Molecular Mechanics Method for Predicting the Conformational Energy of Small Molecules. 194-205 - Pawel Krupa, Anna Halabis, Wioletta Zmudzinska, Stanislaw Oldziej, Harold A. Scheraga, Adam Liwo:
Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. 206
Volume 58, Number 2, February 2018
- Gregor Urban, Niranjan Subrahmanya, Pierre Baldi:
Inner and Outer Recursive Neural Networks for Chemoinformatics Applications. 207-211 - Stephen J. Capuzzi, Thomas E. Thornton, Kammy Liu, Nancy Baker, Wai In Lam, Colin P. O'banion, Eugene N. Muratov, Diane Pozefsky, Alexander Tropsha:
Chemotext: A Publicly Available Web Server for Mining Drug-Target-Disease Relationships in PubMed. 212-218 - Sergio Decherchi, Giovanni Bottegoni, Andrea Spitaleri, Walter Rocchia, Andrea Cavalli:
BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery. 219-224 - Darwin Y. Fu, Jens Meiler:
Predictive Power of Different Types of Experimental Restraints in Small Molecule Docking: A Review. 225-233 - Mark H. Barley, Nicholas J. Turner, Royston Goodacre:
Improved Descriptors for the Quantitative Structure-Activity Relationship Modeling of Peptides and Proteins. 234-243 - Sanghoon Park, Baekjun Kim, Sihoon Choi, Peter G. Boyd, Berend Smit, Jihan Kim:
Text Mining Metal-Organic Framework Papers. 244-251 - Connor W. Coley, Luke Rogers, William H. Green Jr., Klavs F. Jensen:
SCScore: Synthetic Complexity Learned from a Reaction Corpus. 252-261 - Ali Bakiri, Jane Hubert, Romain Reynaud, Carole Lambert, Agathe Martinez, Jean-Hugues Renault, Jean-Marc Nuzillard:
Reconstruction of HMBC Correlation Networks: A Novel NMR-Based Contribution to Metabolite Mixture Analysis. 262-270 - Haoyu S. Yu, Mark A. Watson, Art D. Bochevarov:
Weighted Averaging Scheme and Local Atomic Descriptor for pKa Prediction Based on Density Functional Theory. 271-286 - José Jiménez, Miha Skalic, Gerard Martínez-Rosell, Gianni De Fabritiis:
KDEEP: Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks. 287-296 - Ventsislav Yordanov, Ivan Dimitrov, Irini A. Doytchinova:
Proteochemometrics-Based Prediction of Peptide Binding to HLA-DP Proteins. 297-304 - Sarah E. Graham, Richard D. Smith, Heather A. Carlson:
Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics. 305-314 - Jean-Noël Grad, Alba Gigante, Christoph Wilms, Jan Nikolaj Dybowski, Ludwig Ohl, Christian Ottmann, Carsten Schmuck, Daniel Hoffmann:
Locating Large, Flexible Ligands on Proteins. 315-327 - Soumya Lipsa Rath, Huihui Liu, Susumu Okazaki, Wataru Shinoda:
Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals. 328-337 - Andrew Yeager, Kathryn Humphries, Ellen Farmer, Gene Cline, Bill R. Miller:
Investigation of Nascent Base Pair and Polymerase Behavior in the Presence of Mismatches in DNA Polymerase I Using Molecular Dynamics. 338-349 - Axel Rudling, Adolfo Orro, Jens Carlsson:
Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks. 350-361 - Samira Hezaveh, An-Ping Zeng, Uwe Jandt:
Full Enzyme Complex Simulation: Interactions in Human Pyruvate Dehydrogenase Complex. 362-369 - Souvik Sinha, Atanu Maity, Shubhra Ghosh Dastidar:
BIM Binding Remotely Regulates BAX Activation: Insights from the Free Energy Landscapes. 370-382 - David L. Penkler, Canan Atilgan, Özlem Tastan Bishop:
Allosteric Modulation of Human Hsp90α Conformational Dynamics. 383-404 - Gabrielle Stetz, Gennady M. Verkhivker:
Functional Role and Hierarchy of the Intermolecular Interactions in Binding of Protein Kinase Clients to the Hsp90-Cdc37 Chaperone: Structure-Based Network Modeling of Allosteric Regulation. 405-421 - Yufei Yue, Yue Ma, Ping Qian, Hong Guo:
Catalytic Mechanism of the Ubiquitin-Like NEDD8 Transfer in RING E3-E2∼NEDD8-Target Complex from QM/MM Free Energy Simulations. 422-429 - Huanyu Chu, Haiyan Liu:
TetraBASE: A Side Chain-Independent Statistical Energy for Designing Realistically Packed Protein Backbones. 430-442 - José D. Colbes, Sergio A. Aguila, Carlos A. Brizuela:
Scoring of Side-Chain Packings: An Analysis of Weight Factors and Molecular Dynamics Structures. 443-452 - Swati R. Manjari, Nilesh K. Banavali:
Structural Articulation of Biochemical Reactions Using Restrained Geometries and Topology Switching. 453-463 - Chimno I. Nnadi, Meredith L. Jenkins, Daniel R. Gentile, Leslie A. Bateman, Daniel Zaidman, Trent E. Balius, Daniel K. Nomura, John E. Burke, Kevan M. Shokat, Nir London:
Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange. 464-471 - Alex T. Müller, Jan A. Hiss, Gisbert Schneider:
Recurrent Neural Network Model for Constructive Peptide Design. 472-479 - Hiromasa Kaneko:
Discussion on Regression Methods Based on Ensemble Learning and Applicability Domains of Linear Submodels. 480-489 - Martina Bertazzo, Mattia Bernetti, Maurizio Recanatini, Matteo Masetti, Andrea Cavalli:
Fully Flexible Docking via Reaction-Coordinate-Independent Molecular Dynamics Simulations. 490-500 - Jun Hu, Yang Li, Yang Zhang, Dong-Jun Yu:
ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons. 501-510 - Ari Hardianto, Fei Liu, Shoba Ranganathan:
Molecular Dynamics Pinpoint the Global Fluorine Effect in Balanoid Binding to PKCε and PKA. 511-519 - Kedi Wu, Guo-Wei Wei:
Quantitative Toxicity Prediction Using Topology Based Multitask Deep Neural Networks. 520-531 - Jiawen Chen, Bo Wang, Yinghao Wu:
Structural Characterization and Function Prediction of Immunoglobulin-like Fold in Cell Adhesion and Cell Signaling. 532-542
Volume 58, Number 3, March 2018
- Dimitra-Danai Varsou, Georgia Tsiliki, Penny Nymark, Pekka Kohonen, Roland Grafstrom, Haralambos Sarimveis:
toxFlow: A Web-Based Application for Read-Across Toxicity Prediction Using Omics and Physicochemical Data. 543-549 - Zhihong Liu, Jiewen Du, Xin Yan, Jiali Zhong, Lu Cui, Jinyuan Lin, Lizhu Zeng, Peng Ding, Pin Chen, Xinxin Zhou, Huihao Zhou, Qiong Gu, Jun Xu:
TCMAnalyzer: A Chemo- and Bioinformatics Web Service for Analyzing Traditional Chinese Medicine. 550-555 - Haohao Fu, James C. Gumbart, Haochuan Chen, Xueguang Shao, Wensheng Cai, Christophe Chipot:
BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations. 556-560 - Jaime Rodríguez-Guerra Pedregal, Pablo Gómez-Orellana, Jean-Didier Maréchal:
ESIgen: Electronic Supporting Information Generator for Computational Chemistry Publications. 561-564 - Sereina Riniker:
Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview. 565-578 - Patrick Bleiziffer, Kay Schaller, Sereina Riniker:
Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations. 579-590 - L. Mark Hall, Dennis W. Hill, Kelly Bugden, Shannon Cawley, Lowell H. Hall, Ming-Hui Chen, David F. Grant:
Development of a Reverse Phase HPLC Retention Index Model for Nontargeted Metabolomics Using Synthetic Compounds. 591-604 - Spandana Makeneni, David F. Thieker, Robert J. Woods:
Applying Pose Clustering and MD Simulations To Eliminate False Positives in Molecular Docking. 605-614 - Jason C. Cole, Oliver Korb, Patrick McCabe, Murray G. Read, Robin Taylor:
Knowledge-Based Conformer Generation Using the Cambridge Structural Database. 615-629 - Julian Zaugg, Yosephine Gumulya, Mikael Bodén, Alan E. Mark, Alpeshkumar K. Malde:
Effect of Binding on Enantioselectivity of Epoxide Hydrolase. 630-640 - Álvaro Cortés Cabrera, Paula M. Petrone:
Optimal HTS Fingerprint Definitions by Using a Desirability Function and a Genetic Algorithm. 641-646 - Kartheek Pitta, Marimuthu Krishnan:
Molecular Mechanism, Dynamics, and Energetics of Protein-Mediated Dinucleotide Flipping in a Mismatched DNA: A Computational Study of the RAD4-DNA Complex. 647-660 - Emel Timuçin, Osman Ugur Sezerman:
Thermostability of the PYL-PP2C Heterodimer Is Dependent on Magnesium: In Silico Insights into the Link between Heat Stress Response and Magnesium Deficiency in Plants. 661-672 - Mukesh Patel, Martyn L. Chilton, Andrea Sartini, Laura Gibson, Chris Barber, Liz Covey-Crump, Katarzyna R. Przybylak, Mark T. D. Cronin, Judith C. Madden:
Assessment and Reproducibility of Quantitative Structure-Activity Relationship Models by the Nonexpert. 673-682 - Gerard Martínez-Rosell, Matt J. Harvey, Gianni De Fabritiis:
Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors. 683-691 - Denis Bucher, Pieter F. W. Stouten, Nicolas Triballeau:
Shedding Light on Important Waters for Drug Design: Simulations versus Grid-Based Methods. 692-699 - Hwangseo Park, Hoi-Yun Jung, Shinmee Mah, Sungwoo Hong:
Systematic Computational Design and Identification of Low Picomolar Inhibitors of Aurora Kinase A. 700-709 - Joana Magalhães, Giannamaria Annunziato, Nina Franko, Marco Pieroni, Barbara Campanini, Agostino Bruno, Gabriele Costantino:
Integration of Enhanced Sampling Methods with Saturation Transfer Difference Experiments to Identify Protein Druggable Pockets. 710-723 - Xinxiang Wang, Di Zhang, Sheng-You Huang:
New Knowledge-Based Scoring Function with Inclusion of Backbone Conformational Entropies from Protein Structures. 724-732 - Hamid Hadi-Alijanvand, Maryam Rouhani:
Partner-Specific Prediction of Protein-Dimer Stability from Unbound Structure of Monomer. 733-745
Volume 58, Number 4, April 2018
- Songling Ma, Sungbo Hwang, Se-Han Lee, William E. Acree Jr., Kyoung Tai No:
Incorporation of Hydrogen Bond Angle Dependency into the Generalized Solvation Free Energy Density Model. 761-772 - Yossa Dwi Hartono, You Xu, Andrey Karshikoff, Lennart Nilsson, Alessandra Villa:
Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids. 773-783 - Phani Ghanakota, Herman van Vlijmen, Woody Sherman, Thijs Beuming:
Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein-Protein Interaction Interfaces. 784-793 - Panagiotis Lagarias, Eleni Vrontaki, George Lambrinidis, Dimitrios Stamatis, Marino Convertino, Gabriella Ortore, Thomas M. Mavromoustakos, Karl Norbert Klotz, Antonios Kolocouris:
Discovery of Novel Adenosine Receptor Antagonists through a Combined Structure- and Ligand-Based Approach Followed by Molecular Dynamics Investigation of Ligand Binding Mode. 794-815 - Xiaozheng Zhang, Fengchao Cui, Hongqian Chen, Tianshu Zhang, Kecheng Yang, Yibo Wang, Zhenyan Jiang, Kenner C. Rice, Linda R. Watkins, Mark R. Hutchinson, Yunqi Li, Yinghua Peng, Xiaohui Wang:
Dissecting the Innate Immune Recognition of Opioid Inactive Isomer (+)-Naltrexone Derived Toll-like Receptor 4 (TLR4) Antagonists. 816-825 - Ramin Ekhteiari Salmas, Philip Seeman, Matthias Stein, Serdar Durdagi:
Structural Investigation of the Dopamine-2 Receptor Agonist Bromocriptine Binding to Dimeric D2HighR and D2LowR States. 826-836 - Xi Chen, Qiang Gan, Changgen Feng, Xia Liu, Qian Zhang:
Virtual Screening of Novel and Selective Inhibitors of Protein Tyrosine Phosphatase 1B over T-Cell Protein Tyrosine Phosphatase Using a Bidentate Inhibition Strategy. 837-847 - Dusan Petrovic, Ansgar Bokel, Matthew Allan, Vlada B. Urlacher, Birgit Strodel:
Simulation-Guided Design of Cytochrome P450 for Chemo- and Regioselective Macrocyclic Oxidation. 848-858 - Tifang Miao, Qinghua Deng, Hui Gao, Xianliang Fu, Shuang Li:
Theoretical Studies on DNA-Cleavage Mechanism of Copper(II) Complexes: Probing Generation of Reactive Oxygen Species. 859-866 - Lucía Romero, Jordi Cano, Julio Gomis-Tena, Beatriz Trénor, Ferran Sanz, Manuel Pastor, Javier Saiz:
In Silico QT and APD Prolongation Assay for Early Screening of Drug-Induced Proarrhythmic Risk. 867-878 - Mámon M. Hatmal, Mutasem O. Taha:
Combining Stochastic Deformation/Relaxation and Intermolecular Contacts Analysis for Extracting Pharmacophores from Ligand-Receptor Complexes. 879-893
Volume 58, Number 5, May 2018
- Sharon L. Guffy, Frank D. Teets, Minnie I. Langlois, Brian Kuhlman:
Protocols for Requirement-Driven Protein Design in the Rosetta Modeling Program. 895-901 - Andrew Dalke, Jérôme Hert, Christian Kramer:
mmpdb: An Open-Source Matched Molecular Pair Platform for Large Multiproperty Data Sets. 902-910 - M. Katharine Holloway, Georgia B. McGaughey:
Computational Chemistry: A Rising Tide of Women. 911-915 - Izhar Wallach, Abraham Heifets:
Most Ligand-Based Classification Benchmarks Reward Memorization Rather than Generalization. 916-932 - Dipan Ghosh, Uwe Koch, Kamyar Hadian, Michael Sattler, Igor V. Tetko:
Luciferase Advisor: High-Accuracy Model To Flag False Positive Hits in Luciferase HTS Assays. 933-942 - Chuipu Cai, Jiansong Fang, Pengfei Guo, Qi Wang, Huixiao Hong, Javid Moslehi, Feixiong Cheng:
In Silico Pharmacoepidemiologic Evaluation of Drug-Induced Cardiovascular Complications Using Combined Classifiers. 943-956 - Sorin I. Avram, Alina Bora, Liliana Halip, Ramona Curpan:
Modeling Kinase Inhibition Using Highly Confident Data Sets. 957-967 - Wanli You, Chia-en A. Chang:
Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors. 968-981 - Anna S. Kamenik, Uta F. Lessel, Julian E. Fuchs, Thomas Fox, Klaus R. Liedl:
Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization. 982-992 - Fang-Yu Lin, Pedro E. M. Lopes, Edward Harder, Benoît Roux, Alexander D. MacKerell Jr.:
Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator. 993-1004 - Anna Theresa Cavasin, Alexander Hillisch, Felix Uellendahl, Sebastian Schneckener, Andreas H. Göller:
Reliable and Performant Identification of Low-Energy Conformers in the Gas Phase and Water. 1005-1020 - Steven A. Combs, Benjamin K. Mueller, Jens Meiler:
Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta. 1021-1036 - Haiyang Zhang, Chunhua Yin, Yang Jiang, David van der Spoel:
Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models. 1037-1052 - Amy K. Smith, Dmitri K. Klimov:
Binding of Cytotoxic Aβ25-35 Peptide to the Dimyristoylphosphatidylcholine Lipid Bilayer. 1053-1065 - Fei Ye, Weiyao Zhang, Xiaoqing Ye, Jia Jin, Zhengbing Lv, Cheng Luo:
Identification of Selective, Cell Active Inhibitors of Protein Arginine Methyltransferase 5 through Structure-Based Virtual Screening and Biological Assays. 1066-1073 - Mireia Jiménez-Rosés, Minos-Timotheos Matsoukas, Gianluigi Caltabiano, Arnau Cordomí:
Ligand-Triggered Structural Changes in the M2 Muscarinic Acetylcholine Receptor. 1074-1082 - Ekaterina A. Sosnina, Dmitry I. Osolodkin, Eugene V. Radchenko, Sergey B. Sosnin, Vladimir A. Palyulin:
Influence of Descriptor Implementation on Compound Ranking Based on Multiparameter Assessment. 1083-1093 - Noé Sturm, Annachiara Tinivella, Giulio Rastelli:
Exploration and Comparison of the Geometrical and Physicochemical Properties of an αC Allosteric Pocket in the Structural Kinome. 1094-1103 - Jie Xia, Terry-Elinor Reid, Song Wu, Liangren Zhang, Xiang Simon Wang:
Maximal Unbiased Benchmarking Data Sets for Human Chemokine Receptors and Comparative Analysis. 1104-1120 - Claas Strecker, Bernd Meyer:
Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking. 1121-1131 - Fredrik Svensson, Natália Aniceto, Ulf Norinder, Isidro Cortes-Ciriano, Ola Spjuth, Lars Carlsson, Andreas Bender:
Conformal Regression for Quantitative Structure-Activity Relationship Modeling - Quantifying Prediction Uncertainty. 1132-1140 - Boris Vishnepolsky, Andrei E. Gabrielian, Alex Rosenthal, Darrell E. Hurt, Michael Tartakovsky, Grigol Managadze, Maya Grigolava, George I. Makhatadze, Malak Pirtskhalava:
Predictive Model of Linear Antimicrobial Peptides Active against Gram-Negative Bacteria. 1141-1151
Volume 58, Number 6, June 2018
- Kenneth M. Merz Jr.:
Investing in the Future. 1153 - Alessandro Pedretti, Angelica Mazzolari, Giulio Vistoli:
WarpEngine, a Flexible Platform for Distributed Computing Implemented in the VEGA Program and Specially Targeted for Virtual Screening Studies. 1154-1160 - Kira A. Armacost:
The Transition from Academia: Overcoming the Barrier to a Career in the Drug Discovery Industry. 1161-1163 - Myungshim Kang, Kaushik Chakraborty, Sharon M. Loverde:
Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes. 1164-1168 - Yingchun Cai, Hongbin Yang, Weihua Li, Guixia Liu,