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

•