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Journal of Chemical Information and Modeling, Volume 53
Volume 53, Number 1, January 2013
- Peter Willett:
Combination of Similarity Rankings Using Data Fusion. 1-10
- 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
- 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
- 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
- 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:
FINDSITEcomb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach. 230-240
- Kota Kasahara
, Matsuyuki Shirota, Kengo Kinoshita:
Comprehensive Classification and Diversity Assessment of Atomic Contacts in Protein-Small Ligand Interactions. 241-248
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Stephen R. Heller:
WordPerfect Office X6 Software Review. 519
Volume 53, Number 3, March 2013
- 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
- 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
- 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
- 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
- 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
- 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
- Julien C. Thibault, Julio C. Facelli
, Thomas E. Cheatham III:
iBIOMES: Managing and Sharing Biomolecular Simulation Data in a Distributed Environment. 726-736
- 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
- Andrew Anighoro, Giulio Rastelli
:
Enrichment Factor Analyses on G-Protein Coupled Receptors with Known Crystal Structure. 739-743
- 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
- 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
- Pablo Carbonell
, Lars Carlsson, Jean-Loup Faulon
:
Stereo Signature Molecular Descriptor. 887-897
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- W. Patrick Walters:
Modeling, Informatics, and the Quest for Reproducibility. 1529-1530
- 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
- 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 A2A 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 A2A Antagonists as a Case Study. 1700-1713 - Mark Z. Griffiths, Paul L. A. Popelier:
Characterization of Heterocyclic Rings through Quantum Chemical Topology. 1714-1725
- 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
- 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
- Mikko J. Vainio
, Thierry Kogej, Florian Raubacher, Jens Sadowski:
Scaffold Hopping by Fragment Replacement. 1825-1835
Volume 53, Number 8, August 2013
- Heather A. Carlson
:
Check Your Confidence: Size Really Does Matter. 1837-1841
- 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
- David Zilian, Christoph A. Sotriffer:
SFCscoreRF: A Random Forest-Based Scoring Function for Improved Affinity Prediction of Protein-Ligand Complexes. 1923-1933
- Khaled M. Elokely
, Robert J. Doerksen
:
Docking Challenge: Protein Sampling and Molecular Docking Performance. 1934-1945
- 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
- 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
- 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
- Ragul Gowthaman
, Eric J. Deeds, John Karanicolas:
Structural Properties of Non-Traditional Drug Targets Present New Challenges for Virtual Screening. 2073-2081
- 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
- Leihong Wu
, Ni Ai, Yufeng Liu, Yi Wang, Xiaohui Fan
:
Relating Anatomical Therapeutic Indications by the Ensemble Similarity of Drug Sets. 2154-2160
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 A2A 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Julian E. Fuchs, Klaus R. Liedl
:
Substrate Sequences Tell Similar Stories as Binding Cavities: Commentary. 3115-3116
- 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
- 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
- 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 A2B 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-HT1AR: Discovery of Novel 5-HT1AR 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
- 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
- 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
- Murat Can Cobanoglu, Chang Liu, Feizhuo Hu, Zoltán N. Oltvai, Ivet Bahar:
Predicting Drug-Target Interactions Using Probabilistic Matrix Factorization. 3399-3409
- 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
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