Journal of Chemical Information and Modeling, Volume 53

Volume 53, Number 1, January 2013

Perspectives

• 
  Peter Willett:
  Combination of Similarity Rankings Using Data Fusion. 1-10

Chemical Information

• 
  Chao Ma, Lirong Wang, Peng Yang, Kyaw Z. Myint, Xiang-Qun Xie:
  LiCABEDS II. Modeling of Ligand Selectivity for G-Protein-Coupled Cannabinoid Receptors. 11-26
• 
  Stephan C. Schürer, Steven M. Muskal:
  Kinome-wide Activity Modeling from Diverse Public High-Quality Data Sets. 27-38
• 
  Jonathan B. Baell:
  Broad Coverage of Commercially Available Lead-like Screening Space with Fewer than 350, 000 Compounds. 39-55
• 
  Lars Ruddigkeit, Lorenz C. Blum, Jean-Louis Reymond:
  Visualization and Virtual Screening of the Chemical Universe Database GDB-17. 56-65

Computational Chemistry

• 
  Stefano Alcaro, Sandro Giuseppe Chiodo, Monica Leopoldini, Francesco Ortuso:
  Antioxidant Efficiency of Oxovitisin, a New Class of Red Wine Pyranoanthocyanins, Revealed through Quantum Mechanical Investigations. 66-75
• 
  Sascha Urbaczek, Adrian Kolodzik, Inken Groth, Stefan Heuser, Matthias Rarey:
  Reading PDB: Perception of Molecules from 3D Atomic Coordinates. 76-87
• 
  Laurent Hoffer, Dragos Horvath:
  S4MPLE - Sampler For Multiple Protein-Ligand Entities: Simultaneous Docking of Several Entities. 88-102

Computational Biochemistry

• 
  Ágnes Peragovics, Zoltán Simon, László Tombor, Balázs Jelinek, Péter Hári, Pál Czobor, András Málnási-Csizmadia:
  Virtual Affinity Fingerprints for Target Fishing: A New Application of Drug Profile Matching. 103-113
• 
  Bo Ding, Jian Wang, Nan Li, Wei Wang:
  Characterization of Small Molecule Binding. I. Accurate Identification of Strong Inhibitors in Virtual Screening. 114-122
• 
  Huifang Li, Xin Ren, Eric Leblanc, Kate Frewin, Paul S. Rennie, Artem Cherkasov:
  Identification of Novel Androgen Receptor Antagonists Using Structure- and Ligand-Based Methods. 123-130
• 
  Tuomo Kalliokoski, Tjelvar S. G. Olsson, Anna Vulpetti:
  Subpocket Analysis Method for Fragment-Based Drug Discovery. 131-141
• 
  Chi-Yu Shao, Sing-Zuo Chen, Bo-Han Su, Yufeng J. Tseng, Emilio Xavier Esposito, Anton J. Hopfinger:
  Dependence of QSAR Models on the Selection of Trial Descriptor Sets: A Demonstration Using Nanotoxicity Endpoints of Decorated Nanotubes. 142-158

Pharmaceutical Modeling

• 
  Giovanni Paolo Di Martino, Matteo Masetti, Luisa Ceccarini, Andrea Cavalli, Maurizio Recanatini:
  An Automated Docking Protocol for hERG Channel Blockers. 159-175
• 
  Amit K. Gupta, Kanika Varshney, Neetu Singh, Vaibhav Mishra, Mridula Saxena, Gautam Palit, Anil K. Saxena:
  Identification of Novel Amino Acid Derived CCK-2R Antagonists As Potential Antiulcer Agent: Homology Modeling, Design, Synthesis, and Pharmacology. 176-187
• 
  Xuben Hou, Jintong Du, Jian Zhang, Lupei Du, Hao Fang, Minyong Li:
  How to Improve Docking Accuracy of AutoDock4.2: A Case Study Using Different Electrostatic Potentials. 188-200
• 
  Paulette A. Greenidge, Christian Kramer, Jean-Christophe Mozziconacci, Romain M. Wolf:
  MM/GBSA Binding Energy Prediction on the PDBbind Data Set: Successes, Failures, and Directions for Further Improvement. 201-209
• 
  Weiwei Xue, Xiaojie Jin, Lulu Ning, Meixia Wang, Huanxiang Liu, Xiaojun Yao:
  Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis. 210-222
• 
  Maryam Salahinejad, Tu C. Le, David A. Winkler:
  Capturing the Crystal: Prediction of Enthalpy of Sublimation, Crystal Lattice Energy, and Melting Points of Organic Compounds. 223-229
• 
  Hongyi Zhou, Jeffrey Skolnick:
  FINDSITE^comb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach. 230-240

Bioinformatics

• 
  Kota Kasahara, Matsuyuki Shirota, Kengo Kinoshita:
  Comprehensive Classification and Diversity Assessment of Atomic Contacts in Protein-Small Ligand Interactions. 241-248

Software Description

• 
  Vladimir V. Diky, Robert D. Chirico, Chris Muzny, Andrei F. Kazakov, Kenneth Kroenlein, Joseph W. Magee, Ilmutdin Abdulagatov, Jeong Won Kang, Rafiqul Gani, Michael Frenkel:
  ThermoData Engine (TDE): Software Implementation of the Dynamic Data Evaluation Concept. 8. Properties of Material Streams and Solvent Design. 249-266
• 
  Sunhwan Jo, Wei Jiang, Hui Sun Lee, Benoît Roux, Wonpil Im:
  CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application. 267-277

Volume 53, Number 2, February 2013

Chemical Information

• 
  Xavier Jalencas, Jordi Mestres:
  Chemoisosterism in the Proteome. 279-292
• 
  Nesrine Ben Nasr, Hélène Guillemain, Nathalie Lagarde, Jean-François Zagury, Matthieu Montès:
  Multiple Structures for Virtual Ligand Screening: Defining Binding Site Properties-Based Criteria to Optimize the Selection of the Query. 293-311
• 
  Ye Hu, Jürgen Bajorath:
  Systematic Identification of Scaffolds Representing Compounds Active against Individual Targets and Single or Multiple Target Families. 312-326

Computational Chemistry

• 
  David Kombo, Kartik Tallapragada, Rachit Jain, Joseph Chewning, Anatoly A. Mazurov, Jason D. Speake, Terry A. Hauser, Steve Toler:
  3D Molecular Descriptors Important for Clinical Success. 327-342
• 
  Di Wang, Xuelian Zhu, Changjun Cui, Mei Dong, Hualiang Jiang, Zhengming Li, Zhen Liu, Weiliang Zhu, Jianguo Wang:
  Discovery of Novel Acetohydroxyacid Synthase Inhibitors as Active Agents against Mycobacterium tuberculosis by Virtual Screening and Bioassay. 343-353
• 
  Johannes Kirchmair, Andrew Howlett, Julio E. Peironcely, Daniel S. Murrell, Mark J. Williamson, Samuel E. Adams, Thomas Hankemeier, Leo van Buren, Guus Duchateau, Werner Klaffke, Robert C. Glen:
  How Do Metabolites Differ from Their Parent Molecules and How Are They Excreted? 354-367
• 
  Christopher E. Keefer, Gregory W. Kauffman, Rishi Raj Gupta:
  Interpretable, Probability-Based Confidence Metric for Continuous Quantitative Structure-Activity Relationship Models. 368-383

Computational Biochemistry

• 
  Douglas R. Houston, Malcolm D. Walkinshaw:
  Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context. 384-390
• 
  Katrina W. Lexa, Heather A. Carlson:
  Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data. 391-402
• 
  Mulpuri Nagaraju, Lauren C. McGowan, Donald Hamelberg:
  Cyclophilin A Inhibition: Targeting Transition-State-Bound Enzyme Conformations for Structure-Based Drug Design. 403-410
• 
  Mathias M. von Behren, Andrea Volkamer, Angela M. Henzler, Karen Schomburg, Sascha Urbaczek, Matthias Rarey:
  Fast Protein Binding Site Comparison via an Index-Based Screening Technology. 411-422
• 
  Sohini Basu, Srikanta Sen:
  Do Homologous Thermophilic-Mesophilic Proteins Exhibit Similar Structures and Dynamics at Optimal Growth Temperatures? A Molecular Dynamics Simulation Study. 423-434
• 
  Hajira Ahmed Hotiana, Muhammad K. Haider:
  Structural Modeling of HCV NS3/4A Serine Protease Drug-Resistance Mutations Using End-Point Continuum Solvation and Side-Chain Flexibility Calculations. 435-451
• 
  Shanthi Nagagarajan, Fengtian Xue, Alexander D. MacKerell Jr.:
  Impact of Substrate Protonation and Tautomerization States on Interactions with the Active Site of Arginase I. 452-460

Pharmaceutical Modeling

• 
  Danielle Newby, Alex Alves Freitas, Taravat Ghafourian:
  Coping with Unbalanced Class Data Sets in Oral Absorption Models. 461-474
• 
  Liying Zhang, Denis Fourches, Alexander Sedykh, Hao Zhu, Alexander Golbraikh, Sean Ekins, Julie Clark, Michele C. Connelly, Martina Sigal, Dena Hodges, Armand Guiguemde, R. Kiplin Guy, Alexander Tropsha:
  Discovery of Novel Antimalarial Compounds Enabled by QSAR-Based Virtual Screening. 475-492
• 
  Andrew D. White, Andrew J. Keefe, Ann K. Nowinski, Qing Shao, Kyle Caldwell, Shaoyi Jiang:
  Standardizing and Simplifying Analysis of Peptide Library Data. 493-499

Bioinformatics

• 
  Yaohang Li, Hui Liu, Ionel Rata, Eric Jakobsson:
  Building a Knowledge-Based Statistical Potential by Capturing High-Order Inter-residue Interactions and its Applications in Protein Secondary Structure Assessment. 500-508

Software Description

• 
  Mahendra Awale, Ruud van Deursen, Jean-Louis Reymond:
  MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13. 509-518

Computer Software Reviews

• 
  Stephen R. Heller:
  WordPerfect Office X6 Software Review. 519

Volume 53, Number 3, March 2013

Letters

• 
  Ana Negri, Marie-Laure Rives, Michael J. Caspers, Thomas E. Prisinzano, Jonathan A. Javitch, Marta Filizola:
  Discovery of a Novel Selective Kappa-Opioid Receptor Agonist Using Crystal Structure-Based Virtual Screening. 521-526

Chemical Information

• 
  Miki H. Maeda, Kazumi Kondo:
  Three-Dimensional Structure Database of Natural Metabolites (3DMET): A Novel Database of Curated 3D Structures. 527-533
• 
  N. Yi Mok, Sara Maxe, Ruth Brenk:
  Locating Sweet Spots for Screening Hits and Evaluating Pan-Assay Interference Filters from the Performance Analysis of Two Lead-like Libraries. 534-544
• 
  Ye Hu, Jürgen Bajorath:
  Introduction of Target Cliffs as a Concept To Identify and Describe Complex Molecular Selectivity Patterns. 545-552

Computational Chemistry

• 
  Mohsen Ahmadi, Martin Vogt, Preeti Iyer, Jürgen Bajorath, Holger Fröhlich:
  Predicting Potent Compounds via Model-Based Global Optimization. 553-559
• 
  Tian Zhu, Hyun Lee, Hao Lei, Christopher Jones, Kavankumar Patel, Michael E. Johnson, Kirk E. Hevener:
  Fragment-Based Drug Discovery Using a Multidomain, Parallel MD-MM/PBSA Screening Protocol. 560-572
• 
  Simone Fulle, Chrislaine Withers-Martinez, Michael J. Blackman, Garrett M. Morris, Paul W. Finn:
  Molecular Determinants of Binding to the Plasmodium Subtilisin-like Protease 1. 573-583

Computational Biochemistry

• 
  Hiroshi Izumi, Akihiro Wakisaka, Laurence A. Nafie, Rina K. Dukor:
  Data Mining of Supersecondary Structure Homology between Light Chains of Immunogloblins and MHC Molecules: Absence of the Common Conformational Fragment in the Human IgM Rheumatoid Factor. 584-591
• 
  Guo-Bo Li, Ling-Ling Yang, Wen-Jing Wang, Lin-Li Li, Sheng-Yong Yang:
  ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein-Ligand Interactions. 592-600
• 
  Mai Hamdalla, Ion I. Mandoiu, Dennis W. Hill, Sanguthevar Rajasekaran, David F. Grant:
  BioSM: Metabolomics Tool for Identifying Endogenous Mammalian Biochemical Structures in Chemical Structure Space. 601-612
• 
  Ai Muto, Masaaki Kotera, Toshiaki Tokimatsu, Zenichi Nakagawa, Susumu Goto, Minoru Kanehisa:
  Modular Architecture of Metabolic Pathways Revealed by Conserved Sequences of Reactions. 613-622
• 
  Jérémy Desaphy, Eric Raimbaud, Pierre Ducrot, Didier Rognan:
  Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs. 623-637

Pharmaceutical Modeling

• 
  Marcin Kolaczkowski, Adam Bucki, Marcin Feder, Maciej Pawlowski:
  Ligand-Optimized Homology Models of D₁ and D₂ Dopamine Receptors: Application for Virtual Screening. 638-648
• 
  Marlene Espinoza-Moraga, Nicholas M. Njuguna, Grace Mugumbate, Julio Caballero, Kelly Chibale:
  In silico Comparison of Antimycobacterial Natural Products with Known Antituberculosis Drugs. 649-660
• 
  Fazlin Fauzi, Alexios Koutsoukas, Robert Lowe, Kalpana Joshi, Tai-Ping Fan, Robert C. Glen, Andreas Bender:
  Chemogenomics Approaches to Rationalizing the Mode-of-Action of Traditional Chinese and Ayurvedic Medicines. 661-673
• 
  Achani K. Yatawara, Milan Hodoscek, Dale F. Mierke:
  Ligand Binding Site Identification by Higher Dimension Molecular Dynamics. 674-680
• 
  Kong T. Nguyen, Fengling Li, Gennadiy Poda, David Smil, Masoud Vedadi, Matthieu Schapira:
  Strategy to Target the Substrate Binding site of SET Domain Protein Methyltransferases. 681-691
• 
  Anne Mai Wassermann, Eugen Lounkine, Meir Glick:
  Bioturbo Similarity Searching: Combining Chemical and Biological Similarity To Discover Structurally Diverse Bioactive Molecules. 692-703

Bioinformatics

• 
  Daisuke Takaya, Tomohiro Sato, Hitomi Yuki, Shunta Sasaki, Akiko Tanaka, Shigeyuki Yokoyama, Teruki Honma:
  Prediction of Ligand-Induced Structural Polymorphism of Receptor Interaction Sites Using Machine Learning. 704-716
• 
  Aysam Guerler, Brandon Govindarajoo, Yang Zhang:
  Mapping Monomeric Threading to Protein-Protein Structure Prediction. 717-725

Software Description

• 
  Julien C. Thibault, Julio C. Facelli, Thomas E. Cheatham III:
  iBIOMES: Managing and Sharing Biomolecular Simulation Data in a Distributed Environment. 726-736

Errata

• 
  Maryam Salahinejad, Tu C. Le, David A. Winkler:
  Correction to Capturing the Crystal: Prediction of Enthalpy of Sublimation, Crystal Lattice Energy, and Melting Points of Organic Compounds. 737

Volume 53, Number 4, April 2013

Letters

• 
  Andrew Anighoro, Giulio Rastelli:
  Enrichment Factor Analyses on G-Protein Coupled Receptors with Known Crystal Structure. 739-743

Chemical Information

• 
  Feixiong Cheng, Weihua Li, Xichuan Wang, Yadi Zhou, Zengrui Wu, Jie Shen, Yun Tang:
  Adverse Drug Events: Database Construction and in Silico Prediction. 744-752
• 
  Feixiong Cheng, Weihua Li, Zengrui Wu, Xichuan Wang, Chen Zhang, Jie Li, Guixia Liu, Yun Tang:
  Prediction of Polypharmacological Profiles of Drugs by the Integration of Chemical, Side Effect, and Therapeutic Space. 753-762
• 
  Vladimir I. Chupakhin, Gilles Marcou, Igor I. Baskin, Alexandre Varnek, Didier Rognan:
  Predicting Ligand Binding Modes from Neural Networks Trained on Protein-Ligand Interaction Fingerprints. 763-772
• 
  Tammie L. Borders, Alexandre F. Fonseca, Hengji Zhang, Kyeongjae Cho, Andrew Rusinko III:
  Developing Descriptors To Predict Mechanical Properties of Nanotubes. 773-782
• 
  Robert P. Sheridan:
  Time-Split Cross-Validation as a Method for Estimating the Goodness of Prospective Prediction. 783-790
• 
  Kathrin Heikamp, Jürgen Bajorath:
  Prediction of Compounds with Closely Related Activity Profiles Using Weighted Support Vector Machine Linear Combinations. 791-801

Computational Chemistry

• 
  Ottmar Krämer-Fuhrmann, Jens Neisius, Niklas Gehlen, Dirk Reith, Karl N. Kirschner:
  Wolf₂Pack - Portal Based Atomistic Force-Field Development. 802-808
• 
  Ashutosh Kumar, Akihiro Ito, Mikako Hirohama, Minoru Yoshida, Kam Y. J. Zhang:
  Identification of Sumoylation Activating Enzyme 1 Inhibitors by Structure-Based Virtual Screening. 809-820
• 
  Daniele Pala, Thijs Beuming, Woody Sherman, Alessio Lodola, Silvia Rivara, Marco Mor:
  Structure-Based Virtual Screening of MT₂ Melatonin Receptor: Influence of Template Choice and Structural Refinement. 821-835
• 
  Laurent Hoffer, Jean-Paul Renaud, Dragos Horvath:
  In Silico Fragment-Based Drug Discovery: Setup and Validation of a Fragment-to-Lead Computational Protocol Using S4MPLE. 836-851
• 
  Ilenia Giangreco, David A. Cosgrove, Martin J. Packer:
  An Extensive and Diverse Set of Molecular Overlays for the Validation of Pharmacophore Programs. 852-866
• 
  Kamel Mansouri, Tine Ringsted, Davide Ballabio, Roberto Todeschini, Viviana Consonni:
  Quantitative Structure-Activity Relationship Models for Ready Biodegradability of Chemicals. 867-878
• 
  G. Pilania, C. C. Wang, K. Wu, Nagamani Sukumar, Curt M. Breneman, G. Sotzing, Rampi Ramprasad:
  New Group IV Chemical Motifs for Improved Dielectric Permittivity of Polyethylene. 879-886

Computational Biochemistry

• 
  Pablo Carbonell, Lars Carlsson, Jean-Loup Faulon:
  Stereo Signature Molecular Descriptor. 887-897

Pharmaceutical Modeling

• 
  Garrett M. Morris, Luke G. Green, Zoran Radic, Palmer Taylor, K. Barry Sharpless, Arthur J. Olson, Flavio Grynszpan:
  Automated Docking with Protein Flexibility in the Design of Femtomolar "Click Chemistry" Inhibitors of Acetylcholinesterase. 898-906
• 
  Michelle Lynn Hall, William L. Jorgensen, Lewis Whitehead:
  Automated Ligand- and Structure-Based Protocol for in Silico Prediction of Human Serum Albumin Binding. 907-922
• 
  Irene Kouskoumvekaki, Rasmus K. Petersen, Filip Fratev, Olivier Taboureau, Thomas E. Nielsen, Tudor I. Oprea, Si B. Sonne, Esben N. Flindt, Svava Ósk Jónsdóttir, Karsten Kristiansen:
  Discovery of a Novel Selective PPARγ Ligand with Partial Agonist Binding Properties by Integrated in Silico/in Vitro Work Flow. 923-937
• 
  Yongmei Pan, Yanli Wang, Stephen H. Bryant:
  Pharmacophore and 3D-QSAR Characterization of 6-Arylquinazolin-4-amines as Cdc2-like Kinase 4 (Clk4) and Dual Specificity Tyrosine-phosphorylation-regulated Kinase 1A (Dyrk1A) Inhibitors. 938-947
• 
  Vijay K. Gombar, Stephen D. Hall:
  Quantitative Structure-Activity Relationship Models of Clinical Pharmacokinetics: Clearance and Volume of Distribution. 948-957
• 
  Chia-Yun Chang, Ming-Tsung Hsu, Emilio Xavier Esposito, Yufeng J. Tseng:
  Oversampling to Overcome Overfitting: Exploring the Relationship between Data Set Composition, Molecular Descriptors, and Predictive Modeling Methods. 958-971
• 
  Zhe Li, Ying-Hong Cai, Yuen-Kit Cheng, Xiao Lu, Yong-Xian Shao, Xingshu Li, Ming Liu, Peiqing Liu, Hai-Bin Luo:
  Identification of Novel Phosphodiesterase-4D Inhibitors Prescreened by Molecular Dynamics-Augmented Modeling and Validated by Bioassay. 972-981
• 
  Shunye Zhou, Youyong Li, Tingjun Hou:
  Feasibility of Using Molecular Docking-Based Virtual Screening for Searching Dual Target Kinase Inhibitors. 982-996
• 
  Peichen Pan, Youyong Li, Huidong Yu, Huiyong Sun, Tingjun Hou:
  Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches. 997-1006

Software Description

• 
  Christopher Pfleger, Prakash Chandra Rathi, Doris L. Klein, Sebastian Radestock, Holger Gohlke:
  Constraint Network Analysis (CNA): A Python Software Package for Efficiently Linking Biomacromolecular Structure, Flexibility, (Thermo-)Stability, and Function. 1007-1015

Volume 53, Number 5, May 2013

Chemical Information

• 
  Tobias Girschick, Pedro R. Almeida, Stefan Kramer, Jonna C. Stålring:
  Similarity Boosted Quantitative Structure-Activity Relationship - A Systematic Study of Enhancing Structural Descriptors by Molecular Similarity. 1017-1025
• 
  Faisal Saeed, Naomie Salim, Ammar Abdo:
  Consensus Methods for Combining Multiple Clusterings of Chemical Structures. 1026-1034
• 
  John R. Proudfoot:
  Reaction Schemes Visualized in Network Form: The Syntheses of Strychnine as an Example. 1035-1042
• 
  Arnaud Sinan Karaboga, Jesús M. Planesas, Florent Petronin, Jordi Teixidó, Michel Souchet, Violeta I. Pérez-Nueno:
  Highly SpecIfic and Sensitive Pharmacophore Model for Identifying CXCR4 Antagonists. Comparison with Docking and Shape-Matching Virtual Screening Performance. 1043-1056
• 
  Andreas Bergner, Serge P. Parel:
  Hit Expansion Approaches Using Multiple Similarity Methods and Virtualized Query Structures. 1057-1066
• 
  Dagmar Stumpfe, Dilyana Dimova, Kathrin Heikamp, Jürgen Bajorath:
  Compound Pathway Model To Capture SAR Progression: Comparison of Activity Cliff-Dependent and -Independent Pathways. 1067-1072

Computational Chemistry

• 
  Zheng Zheng, Kenneth M. Merz Jr.:
  Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein-Ligand Interactions. 1073-1083
• 
  Alexander Heifetz, Oliver Barker, Geraldine Verquin, Norbert Wimmer, Wim Meutermans, Sandeep Pal, Richard Law, Mark Whittaker:
  Fighting Obesity with a Sugar-Based Library: Discovery of Novel MCH-1R Antagonists by a New Computational-VAST Approach for Exploration of GPCR Binding Sites. 1084-1099
• 
  Sarah R. Langdon, Isaac M. Westwood, Rob L. M. van Montfort, Nathan Brown, Julian Blagg:
  Scaffold-Focused Virtual Screening: Prospective Application to the Discovery of TTK Inhibitors. 1100-1112
• 
  Mosé Casalegno, Guido Sello:
  Determination of Toxicant Mode of Action by Augmented Top Priority Fragment Class. 1113-1126
• 
  Sairam S. Mallajosyula, Kristie M. Adams, Joseph J. Barchi, Alexander D. MacKerell Jr.:
  Conformational Determinants of the Activity of Antiproliferative Factor Glycopeptide. 1127-1137

Computational Biochemistry

• 
  Divya Ramamoorthy, Edward Turos, Wayne C. Guida:
  Identification of a New Binding Site in E. coli FabH using Molecular Dynamics Simulations: Validation by Computational Alanine Mutagenesis and Docking Studies. 1138-1156
• 
  Wei Cui, Yuanhua Cheng, Lingling Geng, Den-Sheng Liang, Tingjun Hou, Mingjuan Ji:
  Unraveling the Allosteric Inhibition Mechanism of PTP1B by Free Energy Calculation Based on Umbrella Sampling. 1157-1167
• 
  Hui Wen Ng, Charles A. Laughton, Stephen W. Doughty:
  Molecular Dynamics Simulations of the Adenosine A2a Receptor: Structural Stability, Sampling, and Convergence. 1168-1178

Pharmaceutical Modeling

• 
  Bingjie Hu, Markus A. Lill:
  Exploring the Potential of Protein-Based Pharmacophore Models in Ligand Pose Prediction and Ranking. 1179-1190
• 
  Markus K. Dahlgren, Patric Schyman, Julian Tirado-Rives, William L. Jorgensen:
  Characterization of Biaryl Torsional Energetics and its Treatment in OPLS All-Atom Force Fields. 1191-1199

Bioinformatics

• 
  Tomohiro Kinjo, Yuji Koseki, Maiko Kobayashi, Atsumi Yamada, Koji Morita, Kento Yamaguchi, Ryoya Tsurusawa, Gulcin Gulten, Hideyuki Komatsu, Hiroshi Sakamoto, James C. Sacchettini, Mitsuru Kitamura, Shunsuke Aoki:
  Identification of Compounds with Potential Antibacterial Activity against Mycobacterium through Structure-Based Drug Screening. 1200-1212
• 
  Bo Ding, Nan Li, Wei Wang:
  Characterizing Binding of Small Molecules. II. Evaluating the Potency of Small Molecules to Combat Resistance Based on Docking Structures. 1213-1222

Software Description

• 
  Luc Patiny, Alain Borel:
  ChemCalc: A Building Block for Tomorrow's Chemical Infrastructure. 1223-1228
• 
  Tomasz Makarewicz, Rajmund Kazmierkiewicz:
  Molecular Dynamics Simulation by GROMACS Using GUI Plugin for PyMOL. 1229-1234
• 
  Daria B. Kokh, Stefan Richter, Stefan Henrich, Paul Czodrowski, Friedrich Rippmann, Rebecca C. Wade:
  TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins. 1235-1252

Volume 53, Number 6, June 2013

Chemical Information

• 
  Akira Shiraishi, Satoshi Niijima, J. B. Brown, Masahiko Nakatsui, Yasushi Okuno:
  Chemical Genomics Approach for GPCR-Ligand Interaction Prediction and Extraction of Ligand Binding Determinants. 1253-1262
• 
  Antonio de la Vega de León, Jürgen Bajorath:
  Compound Optimization through Data Set-Dependent Chemical Transformations. 1263-1271
• 
  Vigneshwaran Namasivayam, Ye Hu, Jenny Balfer, Jürgen Bajorath:
  Classification of Compounds with Distinct or Overlapping Multi-Target Activities and Diverse Molecular Mechanisms Using Emerging Chemical Patterns. 1272-1281

Computational Chemistry

• 
  Przemyslaw Piechota, Mark T. D. Cronin, Mark Hewitt, Judith C. Madden:
  Pragmatic Approaches to Using Computational Methods To Predict Xenobiotic Metabolism. 1282-1293
• 
  Jonathan D. Tyzack, Mark J. Williamson, Rubben Torella, Robert C. Glen:
  Prediction of Cytochrome P450 Xenobiotic Metabolism: Tethered Docking and Reactivity Derived from Ligand Molecular Orbital Analysis. 1294-1305
• 
  Jinfeng Liu, Xiao He, John Z. H. Zhang:
  Improving the Scoring of Protein-Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization. 1306-1314
• 
  Nopporn Kaiyawet, Thanyada Rungrotmongkol, Supot Hannongbua:
  Effect of Halogen Substitutions on dUMP to Stability of Thymidylate Synthase/dUMP/mTHF Ternary Complex Using Molecular Dynamics Simulation. 1315-1323
• 
  Hongming Chen, Lars Carlsson, Mats Eriksson, Péter L. Várkonyi, Ulf Norinder, Ingemar Nilsson:
  Beyond the Scope of Free-Wilson Analysis: Building Interpretable QSAR Models with Machine Learning Algorithms. 1324-1336
• 
  Sirish Kaushik Lakkaraju, Fengtian Xue, Alan I. Faden, Alexander D. MacKerell Jr.:
  Estimation of Ligand Efficacies of Metabotropic Glutamate Receptors from Conformational Forces Obtained from Molecular Dynamics Simulations. 1337-1349

Computational Biochemistry

• 
  Shan Cong, Xiao-Tu Ma, Yi-Xue Li, Jing-Fang Wang:
  Structural Basis for the Mutation-Induced Dysfunction of Human CYP2J2: A Computational Study. 1350-1357
• 
  Charlotte K. Colenso, Richard B. Sessions, Yi H. Zhang, Jules C. Hancox, Christopher E. Dempsey:
  Interactions between Voltage Sensor and Pore Domains in a hERG K⁺ Channel Model from Molecular Simulations and the Effects of a Voltage Sensor Mutation. 1358-1370
• 
  Duvan Franco, Jacopo Sgrignani, Giovanni Bussi, Alessandra Magistrato:
  Structural Role of Uracil DNA Glycosylase for the Recognition of Uracil in DNA Duplexes. Clues from Atomistic Simulations. 1371-1387

Pharmaceutical Modeling

• 
  Alfonso T. García-Sosa:
  Hydration Properties of Ligands and Drugs in Protein Binding Sites: Tightly-Bound, Bridging Water Molecules and Their Effects and Consequences on Molecular Design Strategies. 1388-1405
• 
  Rafal D. Urniaz, Krzysztof Józwiak:
  X-ray Crystallographic Structures as a Source of Ligand Alignment in 3D-QSAR. 1406-1414
• 
  Martin Smiesko:
  DOLINA - Docking Based on a Local Induced-Fit Algorithm: Application toward Small-Molecule Binding to Nuclear Receptors. 1415-1423
• 
  Senthil Natesan, Zhanbin Wang, Viera Lukacova, Ming Peng, Rajesh Subramaniam, Sandra Lynch, Stefan Balaz:
  Structural Determinants of Drug Partitioning in n-Hexadecane/Water System. 1424-1435
• 
  Laura Goracci, Martina Ceccarelli, Daniela Bonelli, Gabriele Cruciani:
  Modeling Phospholipidosis Induction: Reliability and Warnings. 1436-1446
• 
  Matthias R. Bauer, Tamer M. Ibrahim, Simon M. Vogel, Frank M. Boeckler:
  Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 - A Public Library of Challenging Docking Benchmark Sets. 1447-1462
• 
  Laura Friggeri, Flavio Ballante, Rino Ragno, Ira Musmuca, Daniela de Vita, Fabrizio Manetti, Mariangela Biava, Luigi Scipione, Roberto Di Santo, Roberta Costi, Marta Feroci, Silvano Tortorella:
  Pharmacophore Assessment Through 3-D QSAR: Evaluation of the Predictive Ability on New Derivatives by the Application on a Series of Antitubercular Agents. 1463-1474
• 
  José L. Medina-Franco, Bruce S. Edwards, Clemencia Pinilla, Jon R. Appel, Marc A. Giulianotti, Radleigh Santos, Austin B. Yongye, Larry A. Sklar, Richard A. Houghten:
  Rapid Scanning Structure-Activity Relationships in Combinatorial Data Sets: Identification of Activity Switches. 1475-1485
• 
  Ahmed M. El Kerdawy, Stefan Güssregen, Hans Matter, Matthias Hennemann, Timothy Clark:
  Quantum Mechanics-Based Properties for 3D-QSAR. 1486-1502

Software Description

• 
  Claudia Beato, Andrea Beccari, Carlo Cavazzoni, Simone Lorenzi, Gabriele Costantino:
  Use of Experimental Design To Optimize Docking Performance: The Case of LiGenDock, the Docking Module of Ligen, a New De Novo Design Program. 1503-1517
• 
  Andrea Beccari, Carlo Cavazzoni, Claudia Beato, Gabriele Costantino:
  LiGen: A High Performance Workflow for Chemistry Driven de Novo Design. 1518-1527

Volume 53, Number 7, July 2013

Letters

• 
  W. Patrick Walters:
  Modeling, Informatics, and the Quest for Reproducibility. 1529-1530

Chemical Information

• 
  G. Madhavi Sastry, V. S. Sandeep Inakollu, Woody Sherman:
  Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking. 1531-1542
• 
  Dragos Horvath, Gilles Marcou, Alexandre Varnek:
  Do Not Hesitate to Use Tversky - and Other Hints for Successful Active Analogue Searches with Feature Count Descriptors. 1543-1562
• 
  Alessandro Lusci, Gianluca Pollastri, Pierre Baldi:
  Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules. 1563-1575
• 
  Shana L. Posy, Brian L. Claus, Matt E. Pokross, Stephen R. Johnson:
  3D Matched Pairs: Integrating Ligand- and Structure-Based Knowledge for Ligand Design and Receptor Annotation. 1576-1588
• 
  Bijun Zhang, Ye Hu, Jürgen Bajorath:
  SAR Transfer across Different Targets. 1589-1594
• 
  Kathrin Heikamp, Jürgen Bajorath:
  Comparison of Confirmed Inactive and Randomly Selected Compounds as Negative Training Examples in Support Vector Machine-Based Virtual Screening. 1595-1601
• 
  Martin Vogt, Preeti Iyer, Gerald M. Maggiora, Jürgen Bajorath:
  Conditional Probabilities of Activity Landscape Features for Individual Compounds. 1602-1612
• 
  Martin Vogt, Jürgen Bajorath:
  Similarity Searching for Potent Compounds Using Feature Selection. 1613-1619

Computational Chemistry

• 
  Magdalena Bacilieri, Antonella Ciancetta, Silvia Paoletta, Stephanie Federico, Sandro Cosconati, Barbara Cacciari, Sabrina Taliani, Federico Da Settimo, Ettore Novellino, Karl Norbert Klotz, Giampiero Spalluto, Stefano Moro:
  Revisiting a Receptor-Based Pharmacophore Hypothesis for Human A_2A Adenosine Receptor Antagonists. 1620-1637
• 
  Erik E. Santiso, Nicholas Musolino, Bernhardt L. Trout:
  Design of Linear Ligands for Selective Separation Using a Genetic Algorithm Applied to Molecular Architecture. 1638-1660
• 
  Miroslaw Jablonski, Guglielmo Monaco:
  Different Zeroes of Interaction Energies As the Cause of Opposite Results on the Stabilizing Nature of C-H···O Intramolecular Interactions. 1661-1675
• 
  Hans-Christian Ehrlich, Angela M. Henzler, Matthias Rarey:
  Searching for Recursively Defined Generic Chemical Patterns in Nonenumerated Fragment Spaces. 1676-1688
• 
  Ivan Tubert-Brohman, Woody Sherman, Matthew P. Repasky, Thijs Beuming:
  Improved Docking of Polypeptides with Glide. 1689-1699
• 
  Andrea Bortolato, Benjamin G. Tehan, Michael S. Bodnarchuk, Jonathan W. Essex, Jonathan S. Mason:
  Water Network Perturbation in Ligand Binding: Adenosine A_2A Antagonists as a Case Study. 1700-1713
• 
  Mark Z. Griffiths, Paul L. A. Popelier:
  Characterization of Heterocyclic Rings through Quantum Chemical Topology. 1714-1725

Computational Biochemistry

• 
  Jacob D. Durrant, Aaron J. Friedman, Kathleen Roger, James Andrew McCammon:
  Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening. 1726-1735
• 
  Min Wu, Åke Strid, Leif A. Eriksson:
  Interactions and Stabilities of the UV RESISTANCE LOCUS8 (UVR8) Protein Dimer and Its Key Mutants. 1736-1746
• 
  Ricardo J. Ferreira, Maria-José U. Ferreira, Daniel J. V. A. dos Santos:
  Molecular Docking Characterizes Substrate-Binding Sites and Efflux Modulation Mechanisms within P-Glycoprotein. 1747-1760
• 
  Balaji Selvam, Simon L. Porter, Irina G. Tikhonova:
  Addressing Selective Polypharmacology of Antipsychotic Drugs Targeting the Bioaminergic Receptors through Receptor Dynamic Conformational Ensembles. 1761-1774

Pharmaceutical Modeling

• 
  Hsin-Wen Chang, Fu-Sheng Chung, Chia-Ning Yang:
  Molecular Modeling of p38α Mitogen-Activated Protein Kinase Inhibitors through 3D-QSAR and Molecular Dynamics Simulations. 1775-1786
• 
  Sheng Tian, Youyong Li, Dan Li, Xiaojie Xu, Junmei Wang, Qian Zhang, Tingjun Hou:
  Modeling Compound-Target Interaction Network of Traditional Chinese Medicines for Type II Diabetes Mellitus: Insight for Polypharmacology and Drug Design. 1787-1803
• 
  Gaia Corso, Isabella Coletta, Rosella Ombrato:
  Murine mPGES-1 3D Structure Elucidation and Inhibitors Binding Mode Predictions by Homology Modeling and Site-Directed Mutagenesis. 1804-1817
• 
  Mahesh Kumar Teli, G. Krishnamurthy Rajanikant:
  Computational Repositioning and Experimental Validation of Approved Drugs for HIF-Prolyl Hydroxylase Inhibition. 1818-1824

Software Description

• 
  Mikko J. Vainio, Thierry Kogej, Florian Raubacher, Jens Sadowski:
  Scaffold Hopping by Fragment Replacement. 1825-1835

Volume 53, Number 8, August 2013

2012 CSAR Benchmark Exercise<br />Perspectives

• 
  Heather A. Carlson:
  Check Your Confidence: Size Really Does Matter. 1837-1841

Computational Chemistry

• 
  James B. Dunbar Jr., Richard D. Smith, Kelly L. Damm-Ganamet, Aqeel Ahmed, Emilio Xavier Esposito, James Delproposto, Krishnapriya Chinnaswamy, You-Na Kang, Ginger Kubish, Jason E. Gestwicki, Jeanne A. Stuckey, Heather A. Carlson:
  CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys. 1842-1852
• 
  Kelly L. Damm-Ganamet, Richard D. Smith, James B. Dunbar Jr., Jeanne A. Stuckey, Heather A. Carlson:
  CSAR Benchmark Exercise 2011-2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series. 1853-1870
• 
  Feng Ding, Nikolay V. Dokholyan:
  Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark. 1871-1879
• 
  Ashutosh Kumar, Kam Y. J. Zhang:
  Investigation on the Effect of Key Water Molecules on Docking Performance in CSARdock Exercise. 1880-1892
• 
  David Ryan Koes, Matthew P. Baumgartner, Carlos J. Camacho:
  Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise. 1893-1904
• 
  Sam Z. Grinter, Chengfei Yan, Sheng-You Huang, Lin Jiang, Xiaoqin Zou:
  Automated Large-Scale File Preparation, Docking, and Scoring: Evaluation of ITScore and STScore Using the 2012 Community Structure-Activity Resource Benchmark. 1905-1914
• 
  Denis Fourches, Eugene N. Muratov, Feng Ding, Nikolay V. Dokholyan, Alexander Tropsha:
  Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches. 1915-1922

Computational Biochemistry

• 
  David Zilian, Christoph A. Sotriffer:
  SFCscore^RF: A Random Forest-Based Scoring Function for Improved Affinity Prediction of Protein-Ligand Complexes. 1923-1933

Pharmaceutical Modeling

• 
  Khaled M. Elokely, Robert J. Doerksen:
  Docking Challenge: Protein Sampling and Molecular Docking Performance. 1934-1945

Software Description

• 
  Alexey V. Sulimov, Danil C. Kutov, Igor Oferkin, Ekaterina V. Katkova, Vladimir B. Sulimov:
  Application of the Docking Program SOL for CSAR Benchmark. 1946-1956

Chemical Information

• 
  Alexios Koutsoukas, Robert Lowe, Yasaman KalantarMotamedi, Hamse Y. Mussa, Werner Klaffke, John B. O. Mitchell, Robert C. Glen, Andreas Bender:
  In Silico Target Predictions: Defining a Benchmarking Data Set and Comparison of Performance of the Multiclass Naïve Bayes and Parzen-Rosenblatt Window. 1957-1966
• 
  Xin Yan, Jiabo Li, Zhihong Liu, Minghao Zheng, Hu Ge, Jun Xu:
  Enhancing Molecular Shape Comparison by Weighted Gaussian Functions. 1967-1978
• 
  Julian Schwartz, Mahendra Awale, Jean-Louis Reymond:
  SMIfp (SMILES fingerprint) Chemical Space for Virtual Screening and Visualization of Large Databases of Organic Molecules. 1979-1989
• 
  Igor V. Tetko, Sergii Novotarskyi, Iurii Sushko, Vladimir Ivanov, Alexander E. Petrenko, Reiner Dieden, Florence Lebon, Benoît Mathieu:
  Development of Dimethyl Sulfoxide Solubility Models Using 163 000 Molecules: Using a Domain Applicability Metric to Select More Reliable Predictions. 1990-2000
• 
  Jonna C. Stålring, Pedro Almeida, Lars Carlsson, Ernst Ahlberg Helgee, Catrin Hasselgren Arnby, Scott Boyer:
  Localized Heuristic Inverse Quantitative Structure Activity Relationship with Bulk Descriptors Using Numerical Gradients. 2001-2017

Computational Chemistry

• 
  Rodrigo D. Tosso, Sebastian A. Andujar, Lucas Gutierrez, Emilio Angelina, Ricaurte Rodríguez, Manuel Nogueras, Héctor A. Baldoni, Fernando D. Suvire, Justo Cobo, Ricardo D. Enriz:
  Molecular Modeling Study of Dihydrofolate Reductase Inhibitors. Molecular Dynamics Simulations, Quantum Mechanical Calculations, and Experimental Corroboration. 2018-2032
• 
  Koteswara Rao Valasani, Michael O. Chaney, Victor Day, Shirley ShiDu Yan:
  Acetylcholinesterase Inhibitors: Structure Based Design, Synthesis, Pharmacophore Modeling, and Virtual Screening. 2033-2046
• 
  Jiho Park, Luke Czapla, Rommie E. Amaro:
  Molecular Simulations of Aromatase Reveal New Insights Into the Mechanism of Ligand Binding. 2047-2056
• 
  Qian Zhang, Junmei Wang, Ginés D. Guerrero, José M. Cecilia, José M. García, Youyong Li, Horacio Emilio Pérez Sánchez, Tingjun Hou:
  Accelerated Conformational Entropy Calculations Using Graphic Processing Units. 2057-2064
• 
  Marc Adler, Paul Beroza:
  Improved Ligand Binding Energies Derived from Molecular Dynamics: Replicate Sampling Enhances the Search of Conformational Space. 2065-2072

Computational Biochemistry

• 
  Ragul Gowthaman, Eric J. Deeds, John Karanicolas:
  Structural Properties of Non-Traditional Drug Targets Present New Challenges for Virtual Screening. 2073-2081

Pharmaceutical Modeling

• 
  Serghei Glinca, Gerhard Klebe:
  Cavities Tell More than Sequences: Exploring Functional Relationships of Proteases via Binding Pockets. 2082-2092
• 
  Hao-Peng Sun, Xiaoli Xu, Xiaowen Wu, Xiaojin Zhang, Fang Liu, Jianmin Jia, Xiaoke Guo, Jingjie Huang, Zhengyu Jiang, Taotao Feng, Hongxi Chu, You Zhou, Shenglie Zhang, Zongliang Liu, Qidong You:
  Discovery and Design of Tricyclic Scaffolds as Protein Kinase CK2 (CK2) Inhibitors through a Combination of Shape-Based Virtual Screening and Structure-Based Molecular Modification. 2093-2102
• 
  Chaoqian Cai, Jiayu Gong, Xiaofeng Liu, Daqi Gao, Honglin Li:
  SimG: An Alignment Based Method for Evaluating the Similarity of Small Molecules and Binding Sites. 2103-2115
• 
  Laura Caboni, Billy Egan, Brendan Kelly, Fernando Blanco, Darren Fayne, Mary J. Meegan, David G. Lloyd:
  Structure-Activity Relationships in Non-Ligand Binding Pocket (Non-LBP) Diarylhydrazide Antiandrogens. 2116-2130
• 
  Fung-Yi Chan, Ning Sun, Marco A. C. Neves, Polo Chun-Hung Lam, Wai-Hong Chung, Lai-King Wong, Ho-Yin Chow, Dik-Lung Ma, Pak-Ho Chan, Yun-Chung Leung, Tak-Hang Chan, Ruben Abagyan, Kwok-Yin Wong:
  Identification of a New Class of FtsZ Inhibitors by Structure-Based Design and in Vitro Screening. 2131-2140
• 
  Georgios Leonis, Thomas Steinbrecher, Manthos G. Papadopoulos:
  A Contribution to the Drug Resistance Mechanism of Darunavir, Amprenavir, Indinavir, and Saquinavir Complexes with HIV-1 Protease Due to Flap Mutation I50V: A Systematic MM-PBSA and Thermodynamic Integration Study. 2141-2153

Bioinformatics

• 
  Leihong Wu, Ni Ai, Yufeng Liu, Yi Wang, Xiaohui Fan:
  Relating Anatomical Therapeutic Indications by the Ensemble Similarity of Drug Sets. 2154-2160

Software Description

• 
  Casey W. Bullock, Nicolas Cornia, Reed B. Jacob, Andrew Remm, Thomas Peavey, Ken Weekes, Chris Mallory, Julia T. Oxford, Owen M. McDougal, Timothy L. Andersen:
  DockoMatic 2.0: High Throughput Inverse Virtual Screening and Homology Modeling. 2161-2170
• 
  Xi Cheng, Sunhwan Jo, Hui Sun Lee, Jeffery B. Klauda, Wonpil Im:
  CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems. 2171-2180
• 
  Sheng-Hung Wang, Ying-Ta Wu, Sheng-Chu Kuo, John Yu:
  HotLig: A Molecular Surface-Directed Approach to Scoring Protein-Ligand Interactions. 2181-2195

Volume 53, Number 9, September 2013

Letters

• 
  Alexander Metz, Julia Schanda, Manuel Grez, Christian Wichmann, Holger Gohlke:
  From Determinants of RUNX1/ETO Tetramerization to Small-Molecule Protein-Protein Interaction Inhibitors Targeting Acute Myeloid Leukemia. 2197-2202

Chemical Information

• 
  Masahiko Taniguchi, Hai Du, Jonathan S. Lindsey:
  Enumeration of Virtual Libraries of Combinatorial Modular Macrocyclic (Bracelet, Necklace) Architectures and Their Linear Counterparts. 2203-2216
• 
  Matjaz Depolli, Janez Konc, Kati Rozman, Roman Trobec, Dusanka Janezic:
  Exact Parallel Maximum Clique Algorithm for General and Protein Graphs. 2217-2228
• 
  Todd Martin, Christopher M. Grulke, Douglas M. Young, Christine L. Russom, Nina Y. Wang, Crystal R. Jackson, Mace G. Barron:
  Prediction of Aquatic Toxicity Mode of Action Using Linear Discriminant and Random Forest Models. 2229-2239
• 
  Paul Czodrowski:
  hERG Me Out. 2240-2251
• 
  Jenny Balfer, Martin Vogt, Jürgen Bajorath:
  Searching for Closely Related Ligands with Different Mechanisms of Action Using Machine Learning and Mapping Algorithms. 2252-2274
• 
  Dilyana Dimova, Dagmar Stumpfe, Jürgen Bajorath:
  Quantifying the Fingerprint Descriptor Dependence of Structure-Activity Relationship Information on a Large Scale. 2275-2281

Computational Chemistry

• 
  Gustavo G. Rondina, Juarez L. F. Da Silva:
  Revised Basin-Hopping Monte Carlo Algorithm for Structure Optimization of Clusters and Nanoparticles. 2282-2298
• 
  Shih-Hsun Chen, Sheng-Wei Lin, Shen-Rong Lin, Po-Huang Liang, Jinn-Moon Yang:
  Moiety-Linkage Map Reveals Selective Nonbisphosphonate Inhibitors of Human Geranylgeranyl Diphosphate Synthase. 2299-2311
• 
  Yuling An, Woody Sherman, Steven L. Dixon:
  Kernel-Based Partial Least Squares: Application to Fingerprint-Based QSAR with Model Visualization. 2312-2321
• 
  Jamel Meslamani, Ricky Bhajun, François Martz, Didier Rognan:
  Computational Profiling of Bioactive Compounds Using a Target-Dependent Composite Workflow. 2322-2333
• 
  Marta Erminia Alberto, Cristina Iuga, Angelo Domenico Quartarolo, Nino Russo:
  Bisanthracene Bis(dicarboxylic imide)s as Potential Photosensitizers in Photodynamic Therapy: A Theoretical Investigation. 2334-2340
• 
  Hiromasa Kaneko, Kimito Funatsu:
  Criterion for Evaluating the Predictive Ability of Nonlinear Regression Models without Cross-Validation. 2341-2348

Computational Biochemistry

• 
  Katie L. Whalen, M. Ashley Spies:
  Flooding Enzymes: Quantifying the Contributions of Interstitial Water and Cavity Shape to Ligand Binding Using Extended Linear Response Free Energy Calculations. 2349-2359
• 
  Ting Shi, Yuhui Han, Weihua Li, Yanlong Zhao, Yaqin Liu, Zhimin Huang, Shaoyong Lu, Jian Zhang:
  Exploring the Desumoylation Process of SENP1: A Study Combined MD Simulations with QM/MM Calculations on SENP1-SUMO1-RanGAP1. 2360-2368
• 
  Mohamed A. Helal, Sherief Khalifa, Safwat Ahmed:
  Differential Binding of Latrunculins to G-Actin: A Molecular Dynamics Study. 2369-2375

Pharmaceutical Modeling

• 
  Huiyong Sun, Youyong Li, Dan Li, Tingjun Hou:
  Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches. 2376-2389
• 
  Ivani Pauli, Ricardo N. dos Santos, Diana C. Rostirolla, Leonardo K. Martinelli, Rodrigo G. Ducati, Luís Fernando S. M. Timmers, Luiz Augusto Basso, Diógenes Santiago Santos, Rafael V. C. Guido, Adriano D. Andricopulo, Osmar Norberto de Souza:
  Discovery of New Inhibitors of Mycobacterium tuberculosis InhA Enzyme Using Virtual Screening and a 3D-Pharmacophore-Based Approach. 2390-2401
• 
  Carolina L. Bellera, Darío E. Balcazar, Lucas N. Alberca, Carlos A. Labriola, Alan Talevi, Carolina Carrillo:
  Application of Computer-Aided Drug Repurposing in the Search of New Cruzipain Inhibitors: Discovery of Amiodarone and Bromocriptine Inhibitory Effects. 2402-2408
• 
  Ling Wang, Qiong Gu, Xuehua Zheng, Jiming Ye, Zhihong Liu, Jiabo Li, Xiaopeng Hu, Arnold T. Hagler, Jun Xu:
  Discovery of New Selective Human Aldose Reductase Inhibitors through Virtual Screening Multiple Binding Pocket Conformations. 2409-2422
• 
  Muhammad Yusuf, Janez Konc, Sy Bing Choi, Joanna Trykowska Konc, Nurul Bahiyah Ahmad Khairudin, Dusanka Janezic, Habibah A. Wahab:
  Structurally Conserved Binding Sites of Hemagglutinin as Targets for Influenza Drug and Vaccine Development. 2423-2436

Bioinformatics

• 
  Yan Li, Zhihai Liu, Li Han, Chengke Li, Renxiao Wang:
  Mining the Characteristic Interaction Patterns on Protein-Protein Binding Interfaces. 2437-2447
• 
  Kavyashree Manjunath, Kanagaraj Sekar:
  Molecular Dynamics Perspective on the Protein Thermal Stability: A Case Study Using SAICAR Synthetase. 2448-2461
• 
  Hui Sun Lee, Wonpil Im:
  Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity. 2462-2470

Software Description

• 
  Thomas Gaillard, Benjamin B. L. Schwarz, Yassmine Chebaro, Roland H. Stote, Annick Dejaegere:
  Protein Structural Statistics with PSS. 2471-2482
• 
  Lochana C. Menikarachchi, Dennis W. Hill, Mai Hamdalla, Ion I. Mandoiu, David F. Grant:
  In Silico Enzymatic Synthesis of a 400 000 Compound Biochemical Database for Nontargeted Metabolomics. 2483-2492

Volume 53, Number 10, October 2013

Letters

• 
  Holger Gohlke, Ulrike Hergert, Tatu Meyer, Daniel Mulnaes, Manfred K. Grieshaber, Sander H. J. Smits, Lutz Schmitt:
  Binding Region of Alanopine Dehydrogenase Predicted by Unbiased Molecular Dynamics Simulations of Ligand Diffusion. 2493-2498

Chemical Information

• 
  Pekka Tiikkainen, Louisa J. Bellis, Yvonne Light, Lutz Franke:
  Estimating Error Rates in Bioactivity Databases. 2499-2505
• 
  Shuya Yoshida, Fumiyoshi Yamashita, Atsushi Ose, Kazuya Maeda, Yuichi Sugiyama, Mitsuru Hashida:
  Automated Extraction of Information on Chemical-P-glycoprotein Interactions from the Literature. 2506-2510
• 
  Ana L. Teixeira, André O. Falcão:
  Noncontiguous Atom Matching Structural Similarity Function. 2511-2524

Computational Chemistry

• 
  Nobuyoshi Sugaya:
  Training Based on Ligand Efficiency Improves Prediction of Bioactivities of Ligands and Drug Target Proteins in a Machine Learning Approach. 2525-2537
• 
  Giulio Poli, Tiziano Tuccinardi, Flavio Rizzolio, Isabella Caligiuri, Lorenzo Botta, Carlotta Granchi, Gabriella Ortore, Filippo Minutolo, Silvia Schenone, Adriano Martinelli:
  Identification of New Fyn Kinase Inhibitors Using a FLAP-Based Approach. 2538-2547
• 
  Crina-Maria Ionescu, Stanislav Geidl, Radka Svobodová Vareková, Jaroslav Koca:
  Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. 2548-2558
• 
  Chaitanya A. K. Koppisetty, Martin Frank, Graham J. L. Kemp, Per-Georg Nyholm:
  Computation of Binding Energies Including Their Enthalpy and Entropy Components for Protein-Ligand Complexes Using Support Vector Machines. 2559-2570
• 
  Kamran Haider, David J. Huggins:
  Combining Solvent Thermodynamic Profiles with Functionality Maps of the Hsp90 Binding Site to Predict the Displacement of Water Molecules. 2571-2586
• 
  Mohammad A. Khanfar, Mutasem O. Taha:
  Elaborate Ligand-Based Modeling Coupled with Multiple Linear Regression and k Nearest Neighbor QSAR Analyses Unveiled New Nanomolar mTOR Inhibitors. 2587-2612

Computational Biochemistry

• 
  Radleigh Santos, Marc A. Giulianotti, Richard A. Houghten, José L. Medina-Franco:
  Conditional Probabilistic Analysis for Prediction of the Activity Landscape and Relative Compound Activities. 2613-2625
• 
  Mikko Ylilauri, Olli T. Pentikäinen:
  MMGBSA As a Tool To Understand the Binding Affinities of Filamin-Peptide Interactions. 2626-2633
• 
  Jeffrey R. Van Voorst, Barry C. Finzel:
  Searching for Likeness in a Database of Macromolecular Complexes. 2634-2647
• 
  António César Pimenta, João M. Martins, Ruben Fernandes, Irina S. Moreira:
  Ligand-Induced Structural Changes in TEM-1 Probed by Molecular Dynamics and Relative Binding Free Energy Calculations. 2648-2658
• 
  Bo Wang, Liwei Li, Thomas D. Hurley, Samy O. Meroueh:
  Molecular Recognition in a Diverse Set of Protein-Ligand Interactions Studied with Molecular Dynamics Simulations and End-Point Free Energy Calculations. 2659-2670
• 
  Serge Perato, Jade Fogha, Muriel Sebban, Anne Sophie Voisin-Chiret, Jana Sopkova-de Oliveira Santos, Hassan Oulyadi, Sylvain Rault:
  Conformation Control of Abiotic α-Helical Foldamers. 2671-2680
• 
  Vedat Durmaz, Sebastian Schmidt, Peggy Sabri, Christian Piechotta, Marcus Weber:
  Hands-off Linear Interaction Energy Approach to Binding Mode and Affinity Estimation of Estrogens. 2681-2688
• 
  Luis Morales-Quintana, María Ximena Nuñez-Tobar, María Alejandra Moya-León, Raúl Herrera:
  Molecular Dynamics Simulation and Site-Directed Mutagenesis of Alcohol Acyltransferase: A Proposed Mechanism of Catalysis. 2689-2700

Pharmaceutical Modeling

• 
  Dan Chen, Anirudh Ranganathan, Adriaan P. IJzerman, Gregg Siegal, Jens Carlsson:
  Complementarity between in Silico and Biophysical Screening Approaches in Fragment-Based Lead Discovery against the A_2A Adenosine Receptor. 2701-2714
• 
  Xin Xue, Jin-Lian Wei, Li-Li Xu, Mei-Yang Xi, Xiaoli Xu, Fang Liu, Xiaoke Guo, Lei Wang, Xiaojin Zhang, Ming-Ye Zhang, Meng-Chen Lu, Hao-Peng Sun, Qidong You:
  Effective Screening Strategy Using Ensembled Pharmacophore Models Combined with Cascade Docking: Application to p53-MDM2 Interaction Inhibitors. 2715-2729
• 
  Danielle Newby, Alex Alves Freitas, Taravat Ghafourian:
  Pre-processing Feature Selection for Improved C&RT Models for Oral Absorption. 2730-2742
• 
  Sheng Tian, Huiyong Sun, Youyong Li, Peichen Pan, Dan Li, Tingjun Hou:
  Development and Evaluation of an Integrated Virtual Screening Strategy by Combining Molecular Docking and Pharmacophore Searching Based on Multiple Protein Structures. 2743-2756
• 
  Hu Ge, Yu Wang, Chanjuan Li, Nanhao Chen, Yufang Xie, Mengyan Xu, Yingyan He, Xinchun Gu, Ruibo Wu, Qiong Gu, Liang Zeng, Jun Xu:
  Molecular Dynamics-Based Virtual Screening: Accelerating the Drug Discovery Process by High-Performance Computing. 2757-2764

Bioinformatics

• 
  Guy Haskin Fernald, Russ B. Altman:
  Using Molecular Features of Xenobiotics to Predict Hepatic Gene Expression Response. 2765-2773
• 
  Mark R. Hansen, Hugo O. Villar, Eric Feyfant:
  Development of an Informatics Platform for Therapeutic Protein and Peptide Analytics. 2774-2779

Volume 53, Number 11, November 2013

Perspectives

• 
  Suman Sirimulla, Jake B. Bailey, Rahulsimham Vegesna, Mahesh Narayan:
  Halogen Interactions in Protein-Ligand Complexes: Implications of Halogen Bonding for Rational Drug Design. 2781-2791

Letters

• 
  Rosa Buonfiglio, Mariarosaria Ferraro, Federico Falchi, Andrea Cavalli, Matteo Masetti, Maurizio Recanatini:
  Collecting and Assessing Human Lactate Dehydrogenase-A Conformations for Structure-Based Virtual Screening. 2792-2797

Chemical Information

• 
  Minos-Timotheos Matsoukas, Constantinos Potamitis, Panayiotis Plotas, Maria-Eleni Androutsou, George Agelis, John Matsoukas, Panagiotis Zoumpoulakis:
  Insights into AT₁ Receptor Activation through AngII Binding Studies. 2798-2811
• 
  David Fooshee, Alessio Andronico, Pierre Baldi:
  ReactionMap: An Efficient Atom-Mapping Algorithm for Chemical Reactions. 2812-2819
• 
  Zhi-Luo Deng, Cai-Xia Du, Xiao Li, Ben Hu, Zheng-Kun Kuang, Rong Wang, Shi-Yu Feng, Hong-yu Zhang, De-Xin Kong:
  Exploring the Biologically Relevant Chemical Space for Drug Discovery. 2820-2828
• 
  Sereina Riniker, Nikolas Fechner, Gregory A. Landrum:
  Heterogeneous Classifier Fusion for Ligand-Based Virtual Screening: Or, How Decision Making by Committee Can Be a Good Thing. 2829-2836
• 
  Robert P. Sheridan:
  Using Random Forest To Model the Domain Applicability of Another Random Forest Model. 2837-2850

Computational Chemistry

• 
  Markus Meringer, H. James Cleaves II, Stephen J. Freeland:
  Beyond Terrestrial Biology: Charting the Chemical Universe of α-Amino Acid Structures. 2851-2862
• 
  Alexander Chalikiopoulos, Stefanie Thiele, Mikkel Malmgaard-Clausen, Patrik Rydberg, Vignir Ísberg, Trond Ulven, Thomas M. Frimurer, Mette M. Rosenkilde, David E. Gloriam:
  Structure-Activity Relationships and Identification of Optmized CC-Chemokine Receptor CCR1, 5, and 8 Metal-Ion Chelators. 2863-2873
• 
  Minos-Timotheos Matsoukas, Arnau Cordomí, Santiago Ríos, Leonardo Pardo, Theodore V. Tselios:
  Ligand Binding Determinants for Angiotensin II Type 1 Receptor from Computer Simulations. 2874-2883
• 
  Hans Kraut, Josef Eiblmaier, Guenter Grethe, Peter Löw, Heinz Matuszczyk, Heinz Saller:
  Algorithm for Reaction Classification. 2884-2895
• 
  Johannes Kirchmair, Mark J. Williamson, Avid M. Afzal, Jonathan D. Tyzack, Alison P. K. Choy, Andrew Howlett, Patrik Rydberg, Robert C. Glen:
  FAst MEtabolizer (FAME): A Rapid and Accurate Predictor of Sites of Metabolism in Multiple Species by Endogenous Enzymes. 2896-2907

Computational Biochemistry

• 
  Gunther Lukat, Jens Krüger, Björn Sommer:
  APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories. 2908-2925
• 
  Tim Werner, W. Bret Church:
  Kink Characterization and Modeling in Transmembrane Protein Structures. 2926-2936
• 
  Dario Corrada, Giorgio Colombo:
  Energetic and Dynamic Aspects of the Affinity Maturation Process: Characterizing Improved Variants from the Bevacizumab Antibody with Molecular Simulations. 2937-2950
• 
  Sai Lakshmana Vankayala, Jacqueline C. Hargis, H. Lee Woodcock III:
  How Does Catalase Release Nitric Oxide? A Computational Structure-Activity Relationship Study. 2951-2961
• 
  Kristin Blacklock, Gennady Verkhivker:
  Experimentally Guided Structural Modeling and Dynamics Analysis of Hsp90-p53 Interactions: Allosteric Regulation of the Hsp90 Chaperone by a Client Protein. 2962-2978
• 
  Catarina A. Carvalheda, Sara R. R. Campos, Miguel Machuqueiro, António M. Baptista:
  Structural Effects of pH and Deacylation on Surfactant Protein C in an Organic Solvent Mixture: A Constant-pH MD Study. 2979-2989

Pharmaceutical Modeling

• 
  Ákos Tarcsay, Gábor Paragi, Márton Vass, Balázs Jójárt, Ferenc Bogár, György M. Keserü:
  The Impact of Molecular Dynamics Sampling on the Performance of Virtual Screening against GPCRs. 2990-2999
• 
  Qian Ru, Hala M. Fadda, Chung Li, Daniel Paul, Peng T. Khaw, Steve Brocchini, Mire Zloh:
  Molecular Dynamic Simulations of Ocular Tablet Dissolution. 3000-3008
• 
  Jiansong Fang, Ranyao Yang, Li Gao, Dan Zhou, Shengqian Yang, Ai-lin Liu, Guan-hua Du:
  Predictions of BuChE Inhibitors Using Support Vector Machine and Naive Bayesian Classification Techniques in Drug Discovery. 3009-3020
• 
  Vigneshwari Subramanian, Peteris Prusis, Lars-Olof Pietilä, Henri Xhaard, Gerd Wohlfahrt:
  Visually Interpretable Models of Kinase Selectivity Related Features Derived from Field-Based Proteochemometrics. 3021-3030
• 
  Khaled H. Barakat, John Law, Alessio Prunotto, Wendy C. Magee, David H. Evans, D. Lorne Tyrrell, Jack A. Tuszynski, Michael Houghton:
  Detailed Computational Study of the Active Site of the Hepatitis C Viral RNA Polymerase to Aid Novel Drug Design. 3031-3043
• 
  Yi-You Huang, Zhe Li, Ying-Hong Cai, Ling-Jun Feng, Yinuo Wu, Xingshu Li, Hai-Bin Luo:
  The Molecular Basis for the Selectivity of Tadalafil toward Phosphodiesterase 5 and 6: A Modeling Study. 3044-3053
• 
  Sean Ekins, Joel S. Freundlich, Robert C. Reynolds:
  Fusing Dual-Event Data Sets for Mycobacterium tuberculosis Machine Learning Models and Their Evaluation. 3054-3063

Bioinformatics

• 
  Claudia Andreini, Gabriele Cavallaro, Antonio Rosato, Yana Valasatava:
  MetalS²: A Tool for the Structural Alignment of Minimal Functional Sites in Metal-Binding Proteins and Nucleic Acids. 3064-3075
• 
  Qian Liu, Chee Keong Kwoh, Jinyan Li:
  Binding Affinity Prediction for Protein-Ligand Complexes Based on β Contacts and B Factor. 3076-3085

Software Description

• 
  Dong-Sheng Cao, Yi-Zeng Liang, Jun Yan, Gui-Shan Tan, Qing-Song Xu, Shao Liu:
  PyDPI: Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies. 3086-3096
• 
  Michal Brylinski:
  Nonlinear Scoring Functions for Similarity-Based Ligand Docking and Binding Affinity Prediction. 3097-3112

Errata

• 
  Hiromasa Kaneko, Masamoto Arakawa, Kimito Funatsu:
  Erratum for "Development of a New Regression Analysis Method Using Independent Component Analysis". 3113

Volume 53, Number 12, December 2013

Editorial

• 
  Julian E. Fuchs, Klaus R. Liedl:
  Substrate Sequences Tell Similar Stories as Binding Cavities: Commentary. 3115-3116

Letters

• 
  Luca Bellucci, Lucilla Angeli, Andrea Tafi, Marco Radi, Maurizio Botta:
  Unconventional Plasticity of HIV-1 Reverse Transcriptase: How Inhibitors Could Open a Connection "Gate" between Allosteric and Catalytic Sites. 3117-3122
• 
  Ignasi Buch, Noelia Ferruz, Gianni De Fabritiis:
  Computational Modeling of an Epidermal Growth Factor Receptor Single-Mutation Resistance to Cetuximab in Colorectal Cancer Treatment. 3123-3126

Chemical Information

• 
  Peter J. Sadowski, Pierre Baldi:
  Small-Molecule 3D Structure Prediction Using Open Crystallography Data. 3127-3130
• 
  Vigneshwaran Namasivayam, Preeti Iyer, Jürgen Bajorath:
  Prediction of Individual Compounds Forming Activity Cliffs Using Emerging Chemical Patterns. 3131-3139

Computational Chemistry

• 
  Isis Bonet, Pedro Franco-Montero, Virginia Rivero, Marta Teijeira, Fernanda Borges, Eugenio Uriarte, Aliuska Morales Helguera:
  Classifier Ensemble Based on Feature Selection and Diversity Measures for Predicting the Affinity of A_2B Adenosine Receptor Antagonists. 3140-3155
• 
  Steven R. Shave, Manfred Auer:
  CSBB-ConeExclusion, Adapting Structure Based Solution Virtual Screening to Libraries on Solid Support. 3156-3162
• 
  Yanmin Zhang, Shangyan Yang, Yu Jiao, Haichun Liu, Haoliang Yuan, Shuai Lu, Ting Ran, Sihui Yao, Zhipeng Ke, Jinxing Xu, Xiao Xiong, Yadong Chen, Tao Lu:
  An Integrated Virtual Screening Approach for VEGFR-2 Inhibitors. 3163-3177
• 
  Andreas Lange, Markus O. Zimmermann, Rainer Wilcken, Stefan Zahn, Frank M. Boeckler:
  Targeting Histidine Side Chains in Molecular Design through Nitrogen-Halogen Bonds. 3178-3189
• 
  Irene Díaz, Elías F. Combarro, Pasquale Marinaro, Luigi Troiano:
  Ranking COMMPS Chemical Substances by an Improved POT/RLE Approach. 3190-3201
• 
  Lili Xu, Shanglin Zhou, Kunqian Yu, Bo Gao, Hualiang Jiang, Xuechu Zhen, Wei Fu:
  Molecular Modeling of the 3D Structure of 5-HT_1AR: Discovery of Novel 5-HT_1AR Agonists via Dynamic Pharmacophore-Based Virtual Screening. 3202-3211
• 
  David Kombo, Merouane Bencherif:
  Comparative Study on the Use of Docking and Bayesian Categorization To Predict Ligand Binding to Nicotinic Acetylcholine Receptors (nAChRs) Subtypes. 3212-3222
• 
  Tihomir Tomasic, Basil Hartzoulakis, Nace Zidar, Fiona Chan, Robert W. Kirby, David Madge, Steve Peigneur, Jan Tytgat, Danijel Kikelj:
  Ligand- and Structure-Based Virtual Screening for Clathrodin-Derived Human Voltage-Gated Sodium Channel Modulators. 3223-3232
• 
  Rafal Kurczab, Andrzej J. Bojarski:
  New Strategy for Receptor-Based Pharmacophore Query Construction: A Case Study for 5-HT₇ Receptor Ligands. 3233-3243
• 
  Qingda Zang, Daniel M. Rotroff, Richard S. Judson:
  Binary Classification of a Large Collection of Environmental Chemicals from Estrogen Receptor Assays by Quantitative Structure-Activity Relationship and Machine Learning Methods. 3244-3261
• 
  Ahmed M. El Kerdawy, Christofer S. Tautermann, Timothy Clark, Thomas Fox:
  Economical and Accurate Protocol for Calculating Hydrogen-Bond-Acceptor Strengths. 3262-3272
• 
  Sathish Kumar Ramakrishnan, Marta Martin, Thierry Cloitre, Lucyna Firlej, Frédéric J. G. Cuisinier, Csilla Gergely:
  Insights on the Facet Specific Adsorption of Amino Acids and Peptides toward Platinum. 3273-3279

Computational Biochemistry

• 
  Jun Zhao, Chao Zhao, Guizhao Liang, Mingzhen Zhang, Jie Zheng:
  Engineering Antimicrobial Peptides with Improved Antimicrobial and Hemolytic Activities. 3280-3296
• 
  Qi Chen, John K. Buolamwini, Jeremy C. Smith, Aixiu Li, Qin Xu, Xiaolin Cheng, Dongqing Wei:
  Impact of Resistance Mutations on Inhibitor Binding to HIV-1 Integrase. 3297-3307
• 
  Ying-Lu Cui, Qing-Chuan Zheng, Ji-Long Zhang, Qiao Xue, Yan Wang, Hong-Xing Zhang:
  Molecular Dynamic Investigations of the Mutational Effects on Structural Characteristics and Tunnel Geometry in CYP17A1. 3308-3317

Pharmaceutical Modeling

• 
  Héléna A. Gaspar, Gilles Marcou, Dragos Horvath, Alban Arrault, Sylvain Lozano, Philippe Vayer, Alexandre Varnek:
  Generative Topographic Mapping-Based Classification Models and Their Applicability Domain: Application to the Biopharmaceutics Drug Disposition Classification System (BDDCS). 3318-3325
• 
  Tomasz Fraczek, Agata Siwek, Piotr Paneth:
  Assessing Molecular Docking Tools for Relative Biological Activity Prediction: A Case Study of Triazole HIV-1 NNRTIs. 3326-3342
• 
  Hui-Yong Sun, Feng-Qin Ji, Liang-Yu Fu, Zhong-Yi Wang, Hong-Yu Zhang:
  Structural and Energetic Analyses of SNPs in Drug Targets and Implications for Drug Therapy. 3343-3351
• 
  Tao-wei Huang, Jed Zaretzki, Charles Bergeron, Kristin P. Bennett, Curt M. Breneman:
  DR-Predictor: Incorporating Flexible Docking with Specialized Electronic Reactivity and Machine Learning Techniques to Predict CYP-Mediated Sites of Metabolism. 3352-3366
• 
  Gwyn S. Skone, Stephen Cameron, Irina Voiculescu:
  Doing a Good Turn: The Use of Quaternions for Rotation in Molecular Docking. 3367-3372
• 
  Jed Zaretzki, Matthew K. Matlock, S. Joshua Swamidass:
  XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks. 3373-3383
• 
  E. Prabhu Raman, Wenbo Yu, Sirish Kaushik Lakkaraju, Alexander D. MacKerell Jr.:
  Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach. 3384-3398

Bioinformatics

• 
  Murat Can Cobanoglu, Chang Liu, Feizhuo Hu, Zoltán N. Oltvai, Ivet Bahar:
  Predicting Drug-Target Interactions Using Probabilistic Matrix Factorization. 3399-3409

Software Description

• 
  Christian Kramer, Tristan Bereau, Alexander Spinn, Klaus R. Liedl, Peter Gedeck, Markus Meuwly:
  Deriving Static Atomic Multipoles from the Electrostatic Potential. 3410-3417
• 
  Vladimir V. Diky, Robert D. Chirico, Chris Muzny, Andrei F. Kazakov, Kenneth Kroenlein, Joseph W. Magee, Ilmutdin Abdulagatov, Michael Frenkel:
  ThermoData Engine (TDE): Software Implementation of the Dynamic Data Evaluation Concept. 9. Extensible Thermodynamic Constraints for Pure Compounds and New Model Developments. 3418-3430