Journal of Chemical Information and Modeling, Volume 56

Volume 56, Number 1, January 2016

Application Notes

• 
  Wolfgang Guba, Agnes Meyder, Matthias Rarey, Jérôme Hert:
  Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules. 1-5

Letters

• 
  Gilles Marcou, Dragos Horvath, Alexandre Varnek:
  Kernel Target Alignment Parameter: A New Modelability Measure for Regression Tasks. 6-11

Chemical Information

• 
  Tobias Lang, Florian Flachsenberg, Ulrike von Luxburg, Matthias Rarey:
  Feasibility of Active Machine Learning for Multiclass Compound Classification. 12-20

Computational Chemistry

• 
  Zunnan Huang, Chung F. Wong:
  Inexpensive Method for Selecting Receptor Structures for Virtual Screening. 21-34
• 
  Zuojun Guo, Atli Thorarensen, Jianwei Che, Li Xing:
  Target the More Druggable Protein States in a Highly Dynamic Protein-Protein Interaction System. 35-45
• 
  Bernhard Knapp, Charlotte M. Deane:
  T-Cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex. 46-53
• 
  Flavio Ballante, Garland R. Marshall:
  An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design. 54-72
• 
  Xinya Han, Xiuyun Zhu, Shuaihua Zhu, Lin Wei, Zongqin Hong, Li Guo, Haifeng Chen, Bo Chi, Yan Liu, Lingling Feng, Yanliang Ren, Jian Wan:
  A Rational Design, Synthesis, Biological Evaluation and Structure-Activity Relationship Study of Novel Inhibitors against Cyanobacterial Fructose-1, 6-bisphosphate Aldolase. 73-81

Computational Biochemistry

• 
  Muhammad Yusuf, Nornisah Mohamed, Suriyati Mohamad, Dusanka Janezic, K. V. Damodaran, Habibah A. Wahab:
  H274Y's Effect on Oseltamivir Resistance: What Happens Before the Drug Enters the Binding Site. 82-100
• 
  Tauanne D. Amarante, Gerald Weber:
  Evaluating Hydrogen Bonds and Base Stacking of Single, Tandem and Terminal GU Mismatches in RNA with a Mesoscopic Model. 101-109
• 
  Nadine Homeyer, Harris Ioannidis, Felix Kolarov, Günter Gauglitz, Christos Zikos, Antonios Kolocouris, Holger Gohlke:
  Interpreting Thermodynamic Profiles of Aminoadamantane Compounds Inhibiting the M2 Proton Channel of Influenza A by Free Energy Calculations. 110-126
• 
  Evelyne Deplazes, Josephine Davies, Alexandre M. J. J. Bonvin, Glenn F. King, Alan E. Mark:
  Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a. 127-138
• 
  Arghya Barman, Crystal Smitherman, Michael Souffrant, Giovanni Gadda, Donald Hamelberg:
  Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins. 139-147
• 
  Norbert Jeszenoi, Mónika Bálint, István Horváth, David van der Spoel, Csaba Hetényi:
  Exploration of Interfacial Hydration Networks of Target-Ligand Complexes. 148-158
• 
  Alexander Heifetz, Ewa I. Chudyk, Laura Gleave, Matteo Aldeghi, Vadim Cherezov, Dmitri G. Fedorov, Philip C. Biggin, Michael J. Bodkin:
  The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR-Ligand Interactions. 159-172

Pharmaceutical Modeling

• 
  Venkat Koushik Pulla, Dinavahi Saketh Sriram, Srikant Viswanadha, Dharmarajan Sriram, Perumal Yogeeswari:
  Energy-Based Pharmacophore and Three-Dimensional Quantitative Structure-Activity Relationship (3D-QSAR) Modeling Combined with Virtual Screening To Identify Novel Small-Molecule Inhibitors of Silent Mating-Type Information Regulation 2 Homologue 1 (SIRT1). 173-187
• 
  Alexander Sebastian Hauser, Björn Windshügel:
  LEADS-PEP: A Benchmark Data Set for Assessment of Peptide Docking Performance. 188-200
• 
  Caitlin E. Scott, Kwang H. Ahn, Steven T. Graf, William A. Goddard III, Debra A. Kendall, Ravinder Abrol:
  Computational Prediction and Biochemical Analyses of New Inverse Agonists for the CB1 Receptor. 201-212
• 
  Patric Schyman, Ruifeng Liu, Anders Wallqvist:
  General Purpose 2D and 3D Similarity Approach to Identify hERG Blockers. 213-222
• 
  Michael Betz, Tobias Wulsdorf, Stefan G. Krimmer, Gerhard Klebe:
  Impact of Surface Water Layers on Protein-Ligand Binding: How Well Are Experimental Data Reproduced by Molecular Dynamics Simulations in a Thermolysin Test Case? 223-233
• 
  Dávid Bajusz, György G. Ferenczy, György M. Keserü:
  Discovery of Subtype Selective Janus Kinase (JAK) Inhibitors by Structure-Based Virtual Screening. 234-247

Bioinformatics

• 
  Stefan Bietz, Matthias Rarey:
  SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles. 248-259

Software Description

• 
  Alain Dequidt, Julien Devémy, Agílio A. H. Pádua:
  Thermalized Drude Oscillators with the LAMMPS Molecular Dynamics Simulator. 260-268

Volume 56, Number 2, February 2016

Perspectives

• 
  Toshio Fujita, David A. Winkler:
  Understanding the Roles of the "Two QSARs". 269-274

Chemical Information

• 
  Alex M. Clark, Krishna Dole, Sean Ekins:
  Open Source Bayesian Models. 3. Composite Models for Prediction of Binned Responses. 275-285
• 
  Tomoyuki Miyao, Hiromasa Kaneko, Kimito Funatsu:
  Inverse QSPR/QSAR Analysis for Chemical Structure Generation (from y to x). 286-299
• 
  Swarit Jasial, Ye Hu, Jürgen Bajorath:
  Assessing the Growth of Bioactive Compounds and Scaffolds over Time: Implications for Lead Discovery and Scaffold Hopping. 300-307

Computational Chemistry

• 
  Trayder Thomas, Yu Fang, Elizabeth Yuriev, David K. Chalmers:
  Ligand Binding Pathways of Clozapine and Haloperidol in the Dopamine D₂ and D₃ Receptors. 308-321
• 
  Jérôme Graton, Jean-Yves Le Questel, Peter Maxwell, Paul L. A. Popelier:
  Hydrogen-Bond Accepting Properties of New Heteroaromatic Ring Chemical Motifs: A Theoretical Study. 322-334
• 
  Andrea Volkamer, Sameh Eid, Samo Turk, Friedrich Rippmann, Simone Fulle:
  Identification and Visualization of Kinase-Specific Subpockets. 335-346
• 
  Takashi Kamachi, Kazunari Yoshizawa:
  Low-Mode Conformational Search Method with Semiempirical Quantum Mechanical Calculations: Application to Enantioselective Organocatalysis. 347-353

Computational Biochemistry

• 
  Joonhyeok Choi, Kwang-Eun Choi, Sung Jean Park, Sun Yeou Kim, Jun-Goo Jee:
  Ensemble-Based Virtual Screening Led to the Discovery of New Classes of Potent Tyrosinase Inhibitors. 354-367
• 
  Aaron T. Frank:
  Can Holo NMR Chemical Shifts be Directly Used to Resolve RNA-Ligand Poses? 368-376
• 
  Drew Gunio, John Froehlig, Katerina Pappas, Uneeke Ferguson, Herschel Wade:
  Solution-Binding and Molecular Docking Approaches Combine to Provide an Expanded View of Multidrug Recognition in the MDR Gene Regulator BmrR. 377-389

Pharmaceutical Modeling

• 
  Kazi Yasin Helal, Mateusz Maciejewski, Elisabet Gregori-Puigjané, Meir Glick, Anne Mai Wassermann:
  Public Domain HTS Fingerprints: Design and Evaluation of Compound Bioactivity Profiles from PubChem's Bioassay Repository. 390-398
• 
  David K. Johnson, John Karanicolas:
  Ultra-High-Throughput Structure-Based Virtual Screening for Small-Molecule Inhibitors of Protein-Protein Interactions. 399-411
• 
  Ádám A. Kelemen, Robert Kiss, György G. Ferenczy, László Kovács, Beáta Flachner, Zsolt Lorincz, György M. Keserü:
  Structure-Based Consensus Scoring Scheme for Selecting Class A Aminergic GPCR Fragments. 412-422

Bioinformatics

• 
  Bian Li, Jeffrey L. Mendenhall, Elizabeth Dong Nguyen, Brian E. Weiner, Axel W. Fischer, Jens Meiler:
  Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins. 423-434

Software Description

• 
  Yan Li, Zhixiong Zhao, Zhihai Liu, Minyi Su, Renxiao Wang:
  AutoT&T v.2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization. 435-453

Volume 56, Number 3, March 2016

Application Notes

• 
  Chris A. Kieslich, James B. Smadbeck, George A. Khoury, Christodoulos A. Floudas:
  conSSert: Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure. 455-461

Chemical Information

• 
  Thomas Böttcher:
  An Additive Definition of Molecular Complexity. 462-470

Computational Chemistry

• 
  Cate Anstöter, Beth A. Caine, Paul L. A. Popelier:
  The AIBLHiCoS Method: Predicting Aqueous pK_a Values from Gas-Phase Equilibrium Bond Lengths. 471-483
• 
  Teresa Kaserer, Riccardo Rigo, Philipp Schuster, Stefano Alcaro, Claudia Sissi, Daniela Schuster:
  Optimized Virtual Screening Workflow for the Identification of Novel G-Quadruplex Ligands. 484-500
• 
  Jabed H. Tomal, William J. Welch, Ruben H. Zamar:
  Exploiting Multiple Descriptor Sets in QSAR Studies. 501-509

Computational Biochemistry

• 
  Yuki Moriya, Takuji Yamada, Shujiro Okuda, Zenichi Nakagawa, Masaaki Kotera, Toshiaki Tokimatsu, Minoru Kanehisa, Susumu Goto:
  Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs. 510-516
• 
  Xuegang Fu, Gang Zhang, Ran Liu, Jing Wei, Daisy Zhang-Negrerie, Xiaodong Jian, Qingzhi Gao:
  Mechanistic Study of Human Glucose Transport Mediated by GLUT1. 517-526
• 
  Shijie Chen, Linjuan Li, Yantao Chen, Junchi Hu, Jingqiu Liu, Yu-Chih Liu, Rongfeng Liu, Yuanyuan Zhang, Fanwang Meng, Kongkai Zhu, Junyan Lu, Mingyue Zheng, Kaixian Chen, Jin Zhang, Hualiang Jiang, Zhiyi Yao, Cheng Luo:
  Identification of Novel Disruptor of Telomeric Silencing 1-like (DOT1L) Inhibitors through Structure-Based Virtual Screening and Biological Assays. 527-534

Pharmaceutical Modeling

• 
  Karan Kapoor, Nicole McGill, Cynthia B. Peterson, Harold V. Meyers, Michael N. Blackburn, Jérôme Baudry:
  Discovery of Novel Nonactive Site Inhibitors of the Prothrombinase Enzyme Complex. 535-547
• 
  Elumalai Pavadai, Farah El Mazouni, Sergio Wittlin, Carmen de Kock, Margaret A. Phillips, Kelly Chibale:
  Identification of New Human Malaria Parasite Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors by Pharmacophore and Structure-Based Virtual Screening. 548-562
• 
  Damian Bartuzi, Agnieszka A. Kaczor, Dariusz Matosiuk:
  Interplay between Two Allosteric Sites and Their Influence on Agonist Binding in Human μ Opioid Receptor. 563-570
• 
  Renato M. Ribeiro-Viana, Anna P. Butera, Eliziane S. Santos, César A. Tischer, Rosemeire B. Alves, Rossimiriam Pereira de Freitas, Luciana Guimaraes, Fernando de Pilla Varotti, Gustavo H. R. Viana, Clebio S. Nascimento Jr.:
  Revealing the Binding Process of New 3-Alkylpyridine Marine Alkaloid Analogue Antimalarials and the Heme Group: An Experimental and Theoretical Investigation. 571-579
• 
  Andrew Anighoro, Jürgen Bajorath:
  Three-Dimensional Similarity in Molecular Docking: Prioritizing Ligand Poses on the Basis of Experimental Binding Modes. 580-587

Bioinformatics

• 
  Alejandro Speck Planche, Valeria V. Kleandrova, Juan M. Ruso, M. N. D. S. Cordeiro:
  First Multitarget Chemo-Bioinformatic Model To Enable the Discovery of Antibacterial Peptides against Multiple Gram-Positive Pathogens. 588-598

Volume 56, Number 4, April 2016

Application Notes

• 
  Pengfei Li, Kenneth M. Merz Jr.:
  MCPB.py: A Python Based Metal Center Parameter Builder. 599-604

Chemical Information

• 
  Brian B. Masek, David S. Baker, Roman J. Dorfman, Karen DuBrucq, Victoria C. Francis, Stephan Nagy, Bree L. Richey, Farhad Soltanshahi:
  Multistep Reaction Based De Novo Drug Design: Generating Synthetically Feasible Design Ideas. 605-620
• 
  Durmus U. Karatay, Jie Zhang, Jeffrey S. Harrison, David S. Ginger:
  Classifying Force Spectroscopy of DNA Pulling Measurements Using Supervised and Unsupervised Machine Learning Methods. 621-629

Computational Chemistry

• 
  Dorota Latek, Marek Bajda, Slawomir Filipek:
  A Hybrid Approach to Structure and Function Modeling of G Protein-Coupled Receptors. 630-641
• 
  Dahlia R. Weiss, Andrea Bortolato, Benjamin G. Tehan, Jonathan S. Mason:
  GPCR-Bench: A Benchmarking Set and Practitioners' Guide for G Protein-Coupled Receptor Docking. 642-651
• 
  Jason C. Cole, Colin R. Groom, Oliver Korb, Patrick McCabe, Gregory P. Shields:
  Knowledge-Based Optimization of Molecular Geometries Using Crystal Structures. 652-661
• 
  Gloria Mazzone, Annia Galano, Juan Raúl Alvarez-Idaboy, Nino Russo:
  Coumarin-Chalcone Hybrids as Peroxyl Radical Scavengers: Kinetics and Mechanisms. 662-670

Computational Biochemistry

• 
  Bhumika Arora, Thomas Coudrat, Denise Wootten, Arthur Christopoulos, Santosh B. Noronha, Patrick M. Sexton:
  Prediction of Loops in G Protein-Coupled Receptor Homology Models: Effect of Imprecise Surroundings and Constraints. 671-686
• 
  Alberto Cuzzolin, Mattia Sturlese, Giuseppe Deganutti, Veronica Salmaso, Davide Sabbadin, Antonella Ciancetta, Stefano Moro:
  Deciphering the Complexity of Ligand-Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations. 687-705
• 
  Nadiya Dragneva, Oleg Rubel, Wely B. Floriano:
  Molecular Dynamics of Fibrinogen Adsorption onto Graphene, but Not onto Poly(ethylene glycol) Surface, Increases Exposure of Recognition Sites That Trigger Immune Response. 706-720
• 
  Christopher T. Lee, Jeffrey Comer, Conner Herndon, Nelson Leung, Anna Pavlova, Robert V. Swift, Chris Tung, Christopher N. Rowley, Rommie E. Amaro, Christophe Chipot, Yi Wang, James C. Gumbart:
  Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. 721-733

Pharmaceutical Modeling

• 
  Ashini Bolia, S. Banu Ozkan:
  Adaptive BP-Dock: An Induced Fit Docking Approach for Full Receptor Flexibility. 734-746
• 
  Birgit Waltenberger, Ulrike Garscha, Veronika Temml, Josephine Liers, Oliver Werz, Daniela Schuster, Hermann Stuppner:
  Discovery of Potent Soluble Epoxide Hydrolase (sEH) Inhibitors by Pharmacophore-Based Virtual Screening. 747-762
• 
  Ning-Ning Wang, Jie Dong, Yin-Hua Deng, Min-Feng Zhu, Ming Wen, Zhiqiang Yao, Aiping Lu, Jian-Bing Wang, Dong-Sheng Cao:
  ADME Properties Evaluation in Drug Discovery: Prediction of Caco-2 Cell Permeability Using a Combination of NSGA-II and Boosting. 763-773
• 
  Christoph Grebner, Jessica Iegre, Johan Ulander, Karl Edman, Anders Hogner, Christian Tyrchan:
  Binding Mode and Induced Fit Predictions for Prospective Computational Drug Design. 774-787
• 
  Zhaomin Liu, Joshua Pottel, Moeed Shahamat, Anna Tomberg, Paul Labute, Nicolas Moitessier:
  Elucidating Hyperconjugation from Electronegativity to Predict Drug Conformational Energy in a High Throughput Manner. 788-801
• 
  Saemina Shin, Shinmee Mah, Sungwoo Hong, Hwangseo Park:
  Discovery of Low Micromolar Dual Inhibitors for Wild Type and L1196M Mutant of Anaplastic Lymphoma Kinase through Structure-Based Virtual Screening. 802-810

Software Description

• 
  Suqing Zheng, Qing Tang, Jian He, Shiyu Du, Shaofang Xu, Chaojie Wang, Yong Xu, Fu Lin:
  VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems. 811-818

Errata

• 
  Jin Zhang, Badamkhatan Tuguldur, David van der Spoel:
  Correction to Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation. 819-820

Volume 56, Number 5, May 2016

Chemical Information

• 
  Andreas Barth, Thomas Stengel, Edwin Litterst, Hans Kraut, Henry Matuszczyk, Franz Ailer, Steve Hajkowski:
  A Novel Concept for the Search and Retrieval of the Derwent Markush Resource Database. 821-829

Computational Chemistry

• 
  Robert V. Swift, Siti Azma Jusoh, Tavina L. Offutt, Eric S. Li, Rommie E. Amaro:
  Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles. 830-842

Computational Biochemistry

• 
  Jyothi Padiadpu, Madhulika Mishra, Eshita Sharma, Uchurappa Mala, Kumar Somasundaram, Nagasuma Chandra:
  Probing the Druggability Limits for Enzymes of the NAD Biosynthetic Network in Glioma. 843-853
• 
  Xiao Liu, Jinfeng Liu, Tong Zhu, Lujia Zhang, Xiao He, John Z. H. Zhang:
  PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity. 854-861
• 
  Harris Ioannidis, Antonios Drakopoulos, Christina Tzitzoglaki, Nadine Homeyer, Felix Kolarov, Paraskevi Gkeka, Kathrin Freudenberger, Christos Liolios, Günter Gauglitz, Zoe Cournia, Holger Gohlke, Antonios Kolocouris:
  Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM. 862-876
• 
  Fan Zhang, Nanhao Chen, Ruibo Wu:
  Molecular Dynamics Simulations Elucidate Conformational Dynamics Responsible for the Cyclization Reaction in TEAS. 877-885

Pharmaceutical Modeling

• 
  Daniel Robinson, Thomas Bertrand, Jean-Christophe Carry, Frank Halley, Andreas Karlsson, Magali Mathieu, Hervé Minoux, Marc-Antoine Perrin, Benoit Robert, Laurent Schio, Woody Sherman:
  Differential Water Thermodynamics Determine PI3K-Beta/Delta Selectivity for Solvent-Exposed Ligand Modifications. 886-894
• 
  Alina Bora, Sorin I. Avram, Ionel Ciucanu, Marius Raica, Stefana Avram:
  Predictive Models for Fast and Effective Profiling of Kinase Inhibitors. 895-905
• 
  Yi An, Analise C. Doney, Rodrigo B. Andrade, Steven E. Wheeler:
  Stacking Interactions between 9-Methyladenine and Heterocycles Commonly Found in Pharmaceuticals. 906-914
• 
  Ali Hosseini, Andreu Alibés, Marc Noguera-Julian, Víctor A. Gil, Roger Paredes, Robert Soliva, Modesto Orozco, Victor Guallar:
  Computational Prediction of HIV-1 Resistance to Protease Inhibitors. 915-923
• 
  Siegfried S. F. Leung, Daniel J. Sindhikara, Matthew P. Jacobson:
  Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition. 924-929
• 
  Rukmankesh Mehra, Vikrant Singh Rajput, Monika Gupta, Reena Chib, Amit Kumar, Priya Wazir, Inshad Ali Khan, Amit Nargotra:
  Benzothiazole Derivative as a Novel Mycobacterium tuberculosis Shikimate Kinase Inhibitor: Identification and Elucidation of Its Allosteric Mode of Inhibition. 930-940

Software Description

• 
  Cassio Alves, Federico Iacovelli, Mattia Falconi, Francesca Cardamone, Blasco Morozzo della Rocca, Cristiano L. P. de Oliveira, Alessandro Desideri:
  A Simple and Fast Semiautomatic Procedure for the Atomistic Modeling of Complex DNA Polyhedra. 941-949

Volume 56, Number 6, June 2016

Community Structure Activity Resource (CSAR)
Editorial

• 
  Heather A. Carlson:
  Lessons Learned over Four Benchmark Exercises from the Community Structure-Activity Resource. 951-954

Computational Chemistry

• 
  Hervé Hogues, Traian Sulea, Enrico O. Purisima:
  Evaluation of the Wilma-SIE Virtual Screening Method in Community Structure-Activity Resource 2013 and 2014 Blind Challenges. 955-964
• 
  Ashutosh Kumar, Kam Y. J. Zhang:
  Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise. 965-973
• 
  Philip Prathipati, Kenji Mizuguchi:
  Integration of Ligand and Structure Based Approaches for CSAR-2014. 974-987
• 
  Woong-Hee Shin, Gyu Rie Lee, Chaok Seok:
  Evaluation of GalaxyDock Based on the Community Structure-Activity Resource 2013 and 2014 Benchmark Studies. 988-995
• 
  Virginie Y. Martiny, François Martz, Edithe Selwa, Bogdan I. Iorga:
  Blind Pose Prediction, Scoring, and Affinity Ranking of the CSAR 2014 Dataset. 996-1003
• 
  Matthew P. Baumgartner, Carlos J. Camacho:
  Choosing the Optimal Rigid Receptor for Docking and Scoring in the CSAR 2013/2014 Experiment. 1004-1012
• 
  Chengfei Yan, Sam Z. Grinter, Benjamin Ryan Merideth, Zhiwei Ma, Xiaoqin Zou:
  Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks. 1013-1021
• 
  Richard D. Smith, Kelly L. Damm-Ganamet, James B. Dunbar Jr., Aqeel Ahmed, Krishnapriya Chinnaswamy, James Delproposto, Ginger Kubish, Christine E. Tinberg, Sagar D. Khare, Jiayi Dou, Lindsey Doyle, Jeanne A. Stuckey, David Baker, Heather A. Carlson:
  CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. 1022-1031
• 
  Regina Politi, Marino Convertino, Konstantin I. Popov, Nikolay V. Dokholyan, Alexander Tropsha:
  Docking and Scoring with Target-Specific Pose Classifier Succeeds in Native-Like Pose Identification But Not Binding Affinity Prediction in the CSAR 2014 Benchmark Exercise. 1032-1041

Computational Biochemistry

• 
  Praveen Nedumpully-Govindan, Domen B. Jemec, Feng Ding:
  CSAR Benchmark of Flexible MedusaDock in Affinity Prediction and Nativelike Binding Pose Selection. 1042-1052
• 
  Sergei Grudinin, Petr Popov, Émilie Neveu, Georgy Cheremovskiy:
  Predicting Binding Poses and Affinities in the CSAR 2013-2014 Docking Exercises Using the Knowledge-Based Convex-PL Potential. 1053-1062
• 
  Heather A. Carlson, Richard D. Smith, Kelly L. Damm-Ganamet, Jeanne A. Stuckey, Aqeel Ahmed, Maire A. Convery, Donald O. Somers, Michael Kranz, Patricia A. Elkins, Guanglei Cui, Catherine E. Peishoff, Millard H. Lambert, James B. Dunbar Jr.:
  CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma. 1063-1077

Pharmaceutical Modeling

• 
  Sheng-You Huang, Min Li, Jianxin Wang, Yi Pan:
  HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches. 1078-1087

Bioinformatics

• 
  Xiaolei Zhu, Woong-Hee Shin, Hyungrae Kim, Daisuke Kihara:
  Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein-Ligand Binding Prediction in CSAR 2013 and 2014. 1088-1099

Application Notes

• 
  Roman R. Kapaev, Philip V. Toukach:
  Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software. 1100-1104
• 
  Kai Sommer, Nils-Ole Friedrich, Stefan Bietz, Matthias Hilbig, Therese Inhester, Matthias Rarey:
  UNICON: A Powerful and Easy-to-Use Compound Library Converter. 1105-1111
• 
  Josh Vincent Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, Axel Kohlmeyer:
  TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD. 1112-1116
• 
  Piero Procacci:
  Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations. 1117-1121
• 
  Ramadoss Vijayaraj, François Dehez, Christophe Chipot:
  AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations. 1122-1126

Perspectives

• 
  Paola Gramatica, Alessandro Sangion:
  A Historical Excursus on the Statistical Validation Parameters for QSAR Models: A Clarification Concerning Metrics and Terminology. 1127-1131

Chemical Information

• 
  Chen Jiang, Xi Jin, Ying Dong, Ming Chen:
  Kekule.js: An Open Source JavaScript Chemoinformatics Toolkit. 1132-1138

Computational Chemistry

• 
  David Xu, Samy O. Meroueh:
  Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries. 1139-1151
• 
  Jianping Hu, Zhiwei Feng, Shifan Ma, Yu Zhang, Qin Tong, Mohammed Hamed Alqarni, Xiaojun Gou, Xiang-Qun Xie:
  Difference and Influence of Inactive and Active States of Cannabinoid Receptor Subtype CB2: From Conformation to Drug Discovery. 1152-1163

Computational Biochemistry

• 
  See Hong Chiu, Lei Xie:
  Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics. 1164-1174
• 
  Xia Wang, Chenxu Pan, Jiayu Gong, Xiaofeng Liu, Honglin Li:
  Enhancing the Enrichment of Pharmacophore-Based Target Prediction for the Polypharmacological Profiles of Drugs. 1175-1183
• 
  Jingxu Yang, Hao Liu, Xiaorui Liu, Chengbo Gu, Ray Luo, Hai-Feng Chen:
  Synergistic Allosteric Mechanism of Fructose-1, 6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis. 1184-1192
• 
  Benjamin Bouvier:
  Optimizing the Multivalent Binding of the Bacterial Lectin LecA by Glycopeptide Dendrimers for Therapeutic Purposes. 1193-1204
• 
  Yan Li, Zigang Dong:
  Effect of Clustering Algorithm on Establishing Markov State Model for Molecular Dynamics Simulations. 1205-1215

Pharmaceutical Modeling

• 
  Paolo Tortorella, Antonio Laghezza, Milena Durante, Isabel Gomez-Monterrey, Alessia Bertamino, Pietro Campiglia, Fulvio Loiodice, Simona Daniele, Claudia Martini, Mariangela Agamennone:
  An Effective Virtual Screening Protocol To Identify Promising p53-MDM2 Inhibitors. 1216-1227
• 
  Birgit J. Waldner, Julian E. Fuchs, Michael Schauperl, Christian Kramer, Klaus R. Liedl:
  Protease Inhibitors in View of Peptide Substrate Databases. 1228-1235

Volume 56, Number 7, July 2016

Application Notes

• 
  Tyler W. H. Backman, Thomas Girke:
  bioassayR: Cross-Target Analysis of Small Molecule Bioactivity. 1237-1242

Perspectives

• 
  Denis Fourches, Eugene N. Muratov, Alexander Tropsha:
  Trust, but Verify II: A Practical Guide to Chemogenomics Data Curation. 1243-1252

Chemical Information

• 
  Christos A. Nicolaou, Ian A. Watson, Hong Hu, Ji-Bo Wang:
  The Proximal Lilly Collection: Mapping, Exploring and Exploiting Feasible Chemical Space. 1253-1266

Computational Biochemistry

• 
  Saikat Dutta Chowdhury, Aditya K. Sarkar, Ansuman Lahiri:
  Effect of Inactivating Mutations on Peptide Conformational Ensembles: The Plant Polypeptide Hormone Systemin. 1267-1281
• 
  Zahra Heidari, Daniel R. Roe, Rodrigo Galindo-Murillo, Jahan B. Ghasemi, Thomas E. Cheatham III:
  Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations. 1282-1291
• 
  Traian Sulea, Victor Vivcharuk, Christopher R. Corbeil, Christophe Deprez, Enrico O. Purisima:
  Assessment of Solvated Interaction Energy Function for Ranking Antibody-Antigen Binding Affinities. 1292-1303
• 
  Michael Feig:
  Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD. 1304-1312
• 
  Gaurao V. Dhoke, Yunus Ensari, Mehdi D. Davari, Anna Joëlle Ruff, Ulrich Schwaneberg, Marco Bocola:
  What's My Substrate? Computational Function Assignment of Candida parapsilosis ADH5 by Genome Database Search, Virtual Screening, and QM/MM Calculations. 1313-1323

Pharmaceutical Modeling

• 
  Sébastien Dilly, Jean-François Liégeois:
  Structural Insights into 5-HT_1A/D₄ Selectivity of WAY-100635 Analogues: Molecular Modeling, Synthesis, and in Vitro Binding. 1324-1331
• 
  Sean Ekins, Alexander L. Perryman, Alex M. Clark, Robert C. Reynolds, Joel S. Freundlich:
  Machine Learning Model Analysis and Data Visualization with Small Molecules Tested in a Mouse Model of Mycobacterium tuberculosis Infection (2014-2015). 1332-1343
• 
  Son Tung Ngo, Shang-Ting Fang, Shu-Hsiang Huang, Chao-Liang Chou, Pham Dinh Quoc Huy, Mai Suan Li, Yi-Cheng Chen:
  Anti-arrhythmic Medication Propafenone a Potential Drug for Alzheimer's Disease Inhibiting Aggregation of Aβ: In Silico and in Vitro Studies. 1344-1356
• 
  Cleber C. Melo-Filho, Rafael Ferreira Dantas, Rodolpho C. Braga, Bruno Junior Neves, Mario R. Senger, Walter C. G. Valente, João M. Rezende-Neto, Willian T. Chaves, Eugene N. Muratov, Ross A. Paveley, Nicholas Furnham, Lee Kamentsky, Anne E. Carpenter, Floriano Silva-Junior, Carolina Horta Andrade:
  QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni. 1357-1372
• 
  Markus O. Zimmermann, Andreas Lange, Stefan Zahn, Thomas E. Exner, Frank M. Boeckler:
  Using Surface Scans for the Evaluation of Halogen Bonds toward the Side Chains of Aspartate, Asparagine, Glutamate, and Glutamine. 1373-1383

Bioinformatics

• 
  Reza Aalizadeh, Nikos S. Thomaidis, Anna A. Bletsou, Pablo Gago-Ferrero:
  Quantitative Structure-Retention Relationship Models To Support Nontarget High-Resolution Mass Spectrometric Screening of Emerging Contaminants in Environmental Samples. 1384-1398

Volume 56, Number 8, August 2016

Application Notes

• 
  Vincent Zoete, Antoine Daina, Christophe Bovigny, Olivier Michielin:
  SwissSimilarity: A Web Tool for Low to Ultra High Throughput Ligand-Based Virtual Screening. 1399-1404
• 
  Chin W. Yong:
  Descriptions and Implementations of DL_F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations. 1405-1409

Chemical Information

• 
  Maria Kadukova, Sergei Grudinin:
  Knodle: A Support Vector Machines-Based Automatic Perception of Organic Molecules from 3D Coordinates. 1410-1419
• 
  Kamil Paduszynski:
  In Silico Calculation of Infinite Dilution Activity Coefficients of Molecular Solutes in Ionic Liquids: Critical Review of Current Methods and New Models Based on Three Machine Learning Algorithms. 1420-1437
• 
  Kyrylo Klimenko, Gilles Marcou, Dragos Horvath, Alexandre Varnek:
  Chemical Space Mapping and Structure-Activity Analysis of the ChEMBL Antiviral Compound Set. 1438-1454
• 
  Pavel G. Polishchuk, Oleg Tinkov, Tatiana Khristova, Liudmila Ognichenko, Anna Kosinskaya, Alexandre Varnek, Victor Kuzmin:
  Structural and Physico-Chemical Interpretation (SPCI) of QSAR Models and Its Comparison with Matched Molecular Pair Analysis. 1455-1469

Computational Chemistry

• 
  Alain C. Vaucher, Markus Reiher:
  Molecular Propensity as a Driver for Explorative Reactivity Studies. 1470-1478
• 
  Florent Hédin, Krystel El Hage, Markus Meuwly:
  A Toolkit to Fit Nonbonded Parameters from and for Condensed Phase Simulations. 1479-1489

Computational Biochemistry

• 
  Gabrielle Stetz, Gennady M. Verkhivker:
  Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks. 1490-1517
• 
  Avi Ginsburg, Tal Ben-Nun, Roi Asor, Asaf Shemesh, Israel Ringel, Uri Raviv:
  Reciprocal Grids: A Hierarchical Algorithm for Computing Solution X-ray Scattering Curves from Supramolecular Complexes at High Resolution. 1518-1527
• 
  Tarak Karmakar, Sourav Roy, Hemalatha Balaram, Meher K. Prakash, Sundaram Balasubramanian:
  Product Release Pathways in Human and Plasmodium falciparum Phosphoribosyltransferase. 1528-1538
• 
  Ji-Long Zhang, Qing-Chuan Zheng, Li-Ying Yu, Zheng-Qiang Li, Hong-Xing Zhang:
  Effect of External Electric Field on Substrate Transport of a Secondary Active Transporter. 1539-1546
• 
  Jagna Witek, Bettina G. Keller, Marie-Claude Blatter, Axel Meissner, Trixie Wagner, Sereina Riniker:
  Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. 1547-1562
• 
  Yuanbao Ai, Lingling Yu, Xiao Tan, Xiaoying Chai, Sen Liu:
  Discovery of Covalent Ligands via Noncovalent Docking by Dissecting Covalent Docking Based on a "Steric-Clashes Alleviating Receptor (SCAR)" Strategy. 1563-1575

Pharmaceutical Modeling

• 
  Isidro Cortes-Ciriano:
  Benchmarking the Predictive Power of Ligand Efficiency Indices in QSAR. 1576-1587
• 
  Semen O. Yesylevskyy, Christophe Ramseyer, Marc Pudlo, Jean-René Pallandre, Christophe Borg:
  Selective Inhibition of STAT3 with Respect to STAT1: Insights from Molecular Dynamics and Ensemble Docking Simulations. 1588-1596
• 
  Richard K. Belew, Stefano Forli, David S. Goodsell, T. J. O'Donnell, Arthur J. Olson:
  Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives. 1597-1607

Volume 56, Number 9, September 2016

Application Notes

• 
  Åsmund Ervik, Andrés Mejía, Erich A. Müller:
  Bottled SAFT: A Web App Providing SAFT-γ Mie Force Field Parameters for Thousands of Molecular Fluids. 1609-1614
• 
  Lei Liu, Maria Tsompana, Yong Wang, Dingfeng Wu, Lixin Zhu, Ruixin Zhu:
  Connection Map for Compounds (CMC): A Server for Combinatorial Drug Toxicity and Efficacy Analysis. 1615-1621

Chemical Information

• 
  Shardul Paricharak, Adriaan P. IJzerman, Jeremy L. Jenkins, Andreas Bender, Florian Nigsch:
  Data-Driven Derivation of an "Informer Compound Set" for Improved Selection of Active Compounds in High-Throughput Screening. 1622-1630
• 
  Dragos Horvath, Gilles Marcou, Alexandre Varnek, Shilva Kayastha, Antonio de la Vega de León, Jürgen Bajorath:
  Prediction of Activity Cliffs Using Condensed Graphs of Reaction Representations, Descriptor Recombination, Support Vector Machine Classification, and Support Vector Regression. 1631-1640

Computational Chemistry

• 
  Florian Lauck, Matthias Rarey:
  FSees: Customized Enumeration of Chemical Subspaces with Limited Main Memory Consumption. 1641-1653
• 
  Serge Christmann-Franck, Gerard J. P. van Westen, George Papadatos, Fanny Beltran Escudie, Alexander Roberts, John P. Overington, Daniel Domine:
  Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound-Kinase Activities: A Way toward Selective Promiscuity by Design? 1654-1675
• 
  Woong-Hee Shin, Charles Christoffer, Ji-Bo Wang, Daisuke Kihara:
  PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation. 1676-1691
• 
  Irene Maffucci, Alessandro Contini:
  Improved Computation of Protein-Protein Relative Binding Energies with the Nwat-MMGBSA Method. 1692-1704
• 
  Gonzalo Colmenarejo:
  Compound Prioritization in Single-Concentration Screening Data Using Ligand Efficiency Indexes. 1705-1713
• 
  Annia Galano, Adriana Pérez-González, Romina Castañeda-Arriaga, Leonardo Muñoz-Rugeles, Gabriela Mendoza-Sarmiento, Antonio Romero-Silva, Agustin Ibarra-Escutia, Aida Mariana Rebollar-Zepeda, Jorge Rafael León-Carmona, Manuel Alejandro Hernández-Olivares, Juan Raúl Alvarez-Idaboy:
  Empirically Fitted Parameters for Calculating pK_a Values with Small Deviations from Experiments Using a Simple Computational Strategy. 1714-1724

Computational Biochemistry

• 
  Xiaomin Ma, Hu Meng, Luhua Lai:
  Motions of Allosteric and Orthosteric Ligand-Binding Sites in Proteins are Highly Correlated. 1725-1733
• 
  Yu-Chen Chen, Robert Tolbert, Alex M. Aronov, Georgia B. McGaughey, W. Patrick Walters, Lidio Meireles:
  Prediction of Protein Pairs Sharing Common Active Ligands Using Protein Sequence, Structure, and Ligand Similarity. 1734-1745
• 
  Konrad Krawczyk, Adelene Y. L. Sim, Bernhard Knapp, Charlotte M. Deane, Peter Minary:
  Tertiary Element Interaction in HIV-1 TAR. 1746-1754
• 
  Ping Qian, Hao-Bo Guo, Yufei Yue, Liang Wang, Xiaohan Yang, Hong Guo:
  Understanding the Catalytic Mechanism of Xanthosine Methyltransferase in Caffeine Biosynthesis from QM/MM Molecular Dynamics and Free Energy Simulations. 1755-1761
• 
  Nathalie Duclert-Savatier, Guillaume Bouvier, Michael Nilges, Thérèse E. Malliavin:
  Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa: d-Lac Ligase VanA. 1762-1775
• 
  Jean-Marc Billod, Patricia Saenz-Méndez, Anders Blomberg, Leif A. Eriksson:
  Structures, Properties, and Dynamics of Intermediates in eEF2-Diphthamide Biosynthesis. 1776-1786
• 
  Maria Musgaard, Philip C. Biggin:
  Steered Molecular Dynamics Simulations Predict Conformational Stability of Glutamate Receptors. 1787-1797
• 
  Elke Haensele, Noureldin Saleh, Christopher M. Read, Lee Banting, David C. Whitley, Timothy Clark:
  Can Simulations and Modeling Decipher NMR Data for Conformational Equilibria? Arginine-Vasopressin. 1798-1807
• 
  Zied Gaieb, David D. Lo, Dimitrios Morikis:
  Molecular Mechanism of Biased Ligand Conformational Changes in CC Chemokine Receptor 7. 1808-1822
• 
  Christian Margreitter, Chris Oostenbrink:
  Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting. 1823-1834

Pharmaceutical Modeling

• 
  Maria Zatsepin, Angela Mattes, Steffen Rupp, Doris Finkelmeier, Arijit Basu, Anke Burger-Kentischer, Amiram Goldblum:
  Computational Discovery and Experimental Confirmation of TLR9 Receptor Antagonist Leads. 1835-1846
• 
  Yuan Xu, Liyan Yue, Yulan Wang, Jing Xing, Zhifeng Chen, Zhe Shi, Rongfeng Liu, Yu-Chih Liu, Xiaomin Luo, Hualiang Jiang, Kaixian Chen, Cheng Luo, Mingyue Zheng:
  Discovery of Novel Inhibitors Targeting the Menin-Mixed Lineage Leukemia Interface Using Pharmacophore- and Docking-Based Virtual Screening. 1847-1855
• 
  Myriam Ciordia, Laura Pérez-Benito, Francisca Delgado, Andrés A. Trabanco, Gary Tresadern:
  Application of Free Energy Perturbation for the Design of BACE1 Inhibitors. 1856-1871
• 
  Kelly Mulholland, Chun Wu:
  Computational Study of Anticancer Drug Resistance Caused by 10 Topisomerase I Mutations, Including 7 Camptothecin Analogs and Lucanthone. 1872-1883

Volume 56, Number 10, October 2016

Chemical Information

• 
  Shunichi Takeda, Hiromasa Kaneko, Kimito Funatsu:
  Chemical-Space-Based de Novo Design Method To Generate Drug-Like Molecules. 1885-1893
• 
  Matthew C. Swain, Jacqueline M. Cole:
  ChemDataExtractor: A Toolkit for Automated Extraction of Chemical Information from the Scientific Literature. 1894-1904
• 
  Roberto Todeschini, Davide Ballabio, Francesca Grisoni:
  Beware of Unreliable Q²! A Comparative Study of Regression Metrics for Predictivity Assessment of QSAR Models. 1905-1913
• 
  Sergey Shityakov, Ramin Ekhteiari Salmas, Serdar Durdagi, Ellaine Salvador, Katalin Pápai, Maria Josefa Yáñez-Gascón, Horacio Pérez Sánchez, István Puskás, Norbert Roewer, Carola Förster, Jens-Albert Broscheit:
  Characterization, in Vivo Evaluation, and Molecular Modeling of Different Propofol-Cyclodextrin Complexes To Assess Their Drug Delivery Potential at the Blood-Brain Barrier Level. 1914-1922

Computational Chemistry

• 
  Tavina L. Offutt, Robert V. Swift, Rommie E. Amaro:
  Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations. 1923-1935
• 
  Govindan Subramanian, Bharath Ramsundar, Vijay S. Pande, Rajiah Aldrin Denny:
  Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches. 1936-1949
• 
  Juan Jesús Pérez, Maria Santos Tomás, Jaime Rubio-Martinez:
  Assessment of the Sampling Performance of Multiple-Copy Dynamics versus a Unique Trajectory. 1950-1962
• 
  Stavros Chatzieleftheriou, Matthew R. Adendorff, Nikos D. Lagaros:
  Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures. 1963-1978

Computational Biochemistry

• 
  Zhiqiang Yao, Lujia Zhang, Bei Gao, Dongbing Cui, Fengqing Wang, Xiao He, John Z. H. Zhang, Dongzhi Wei:
  A Semiautomated Structure-Based Method To Predict Substrates of Enzymes via Molecular Docking: A Case Study with Candida antarctica Lipase B. 1979-1994
• 
  Yu Zhang, Lirong Wang, Zhiwei Feng, Haizi Cheng, Terence Francis McGuire, Yahui Ding, Tao Cheng, Yingdai Gao, Xiang-Qun Xie:
  StemCellCKB: An Integrated Stem Cell-Specific Chemogenomics KnowledgeBase for Target Identification and Systems-Pharmacology Research. 1995-2004
• 
  Noriko Shimba, Narutoshi Kamiya, Haruki Nakamura:
  Model Building of Antibody-Antigen Complex Structures Using GBSA Scores. 2005-2012
• 
  Paul Czodrowski, Wolf-Guido Bolick:
  OCEAN: Optimized Cross rEActivity estimatioN. 2013-2023
• 
  Mengdan Qian, Yaming Shan, Shanshan Guan, Hao Zhang, Song Wang, Weiwei Han:
  Structural Basis of Fullerene Derivatives as Novel Potent Inhibitors of Protein Tyrosine Phosphatase 1B: Insight into the Inhibitory Mechanism through Molecular Modeling Studies. 2024-2034
• 
  Athanasia-Panagiota Serafeim, Georgios Salamanos, Kalliopi K. Patapati, Nicholas M. Glykos:
  Sensitivity of Folding Molecular Dynamics Simulations to Even Minor Force Field Changes. 2035-2041

Pharmaceutical Modeling

• 
  Franco Lombardo, Yankang Jing:
  In Silico Prediction of Volume of Distribution in Humans. Extensive Data Set and the Exploration of Linear and Nonlinear Methods Coupled with Molecular Interaction Fields Descriptors. 2042-2052
• 
  Eelke B. Lenselink, Willem Jespers, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen:
  Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening. 2053-2060
• 
  Sujun Qu, Shuheng Huang, Xianchao Pan, Li Yang, Hu Mei:
  Constructing Interconsistent, Reasonable, and Predictive Models for Both the Kinetic and Thermodynamic Properties of HIV-1 Protease Inhibitors. 2061-2068
• 
  Francesca Moraca, Kriti Acharya, Bruno Melillo, Amos B. Smith III, Irwin Chaiken, Cameron F. Abrams:
  Computational Evaluation of HIV-1 gp120 Conformations of Soluble Trimeric gp140 Structures as Targets for de Novo Docking of First- and Second-Generation Small-Molecule CD4 Mimics. 2069-2079
• 
  Haiyang Zhang, Chunhua Yin, Hai Yan, David van der Spoel:
  Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes. 2080-2092
• 
  Kelly Mulholland, Chun Wu:
  Binding of Telomestatin to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent. 2093-2102

Bioinformatics

• 
  Ying Wang, Yingnv Gao, Yan Li, Jia-Ning Wan, Rui-Heng Yang, Wen-Jun Mao, Chen-Li Zhou, Li-Hua Tang, Ming Gong, Ying-Ying Wu, Da-Peng Bao:
  Discovery and Characterization of the Highly Active Fungal Immunomodulatory Protein Fip-vvo82. 2103-2114
• 
  Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang:
  Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines. 2123

Volume 56, Number 11, November 2016

Letters

• 
  Peter J. Sadowski, David Fooshee, Niranjan Subrahmanya, Pierre Baldi:
  Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction. 2125-2128

Chemical Information

• 
  Sara Khan, Umar Farooq, Maria G. Kurnikova:
  Exploring Protein Stability by Comparative Molecular Dynamics Simulations of Homologous Hyperthermophilic, Mesophilic, and Psychrophilic Proteins. 2129-2139
• 
  Arkadii I. Lin, Timur I. Madzhidov, Olga Klimchuk, Ramil I. Nugmanov, Igor S. Antipin, Alexandre Varnek:
  Automatized Assessment of Protective Group Reactivity: A Step Toward Big Reaction Data Analysis. 2140-2148
• 
  Laura Guasch, Waruna Yapamudiyansel, Megan L. Peach, James A. Kelley, Joseph J. Barchi, Marc C. Nicklaus:
  Experimental and Chemoinformatics Study of Tautomerism in a Database of Commercially Available Screening Samples. 2149-2161

Computational Chemistry

• 
  James L. McDonagh, David S. Palmer, Tanja Van Mourik, John B. O. Mitchell:
  Are the Sublimation Thermodynamics of Organic Molecules Predictable? 2162-2179
• 
  Jonathan D. Tyzack, Peter A. Hunt, Matthew D. Segall:
  Predicting Regioselectivity and Lability of Cytochrome P450 Metabolism Using Quantum Mechanical Simulations. 2180-2193
• 
  Qin Wang, Simone Sciabola, Gabriela Barreiro, Xinjun Hou, Guoyun Bai, Michael J. Shapiro, Frank Koehn, Anabella Villalobos, Matthew P. Jacobson:
  Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction. 2194-2206
• 
  Wojciech Pulawski, Michal Jamróz, Michal Kolinski, Andrzej Kolinski, Sebastian Kmiecik:
  Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model. 2207-2215

Computational Biochemistry

• 
  Michelle Lynn Hall, David Calkins, Woody Sherman:
  Automated Protocol for Large-Scale Modeling of Gene Expression Data. 2216-2224

Pharmaceutical Modeling

• 
  Elena Dolgikh, Ian A. Watson, Prashant V. Desai, Geri A. Sawada, Stuart Morton, Timothy M. Jones, Thomas J. Raub:
  QSAR Model of Unbound Brain-to-Plasma Partition Coefficient, K_{p, uu, brain}: Incorporating P-glycoprotein Efflux as a Variable. 2225-2233
• 
  Shufang Yang, Ran Wang, Guang Wan, Zhimin Wu, Shujuan Guo, Xingxing Dai, Xinyuan Shi, Yanjiang Qiao:
  A Multiscale Study on the Penetration Enhancement Mechanism of Menthol to Osthole. 2234-2242
• 
  Brandall L. Ingle, Brandon C. Veber, John W. Nichols, Rogelio Tornero-Velez:
  Informing the Human Plasma Protein Binding of Environmental Chemicals by Machine Learning in the Pharmaceutical Space: Applicability Domain and Limits of Predictability. 2243-2252
• 
  Robert P. Sheridan:
  Debunking the Idea that Ligand Efficiency Indices Are Superior to pIC50 as QSAR Activities. 2253-2262

Bioinformatics

• 
  Magdalena A. Mozolewska, Pawel Krupa, Bartlomiej Zaborowski, Adam Liwo, Jooyoung Lee, Keehyoung Joo, Cezary Czaplewski:
  Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field. 2263-2279

Errata

• 
  Ping Qian, Hao-Bo Guo, Yufei Yue, Liang Wang, Xiaohan Yang, Hong Guo:
  Correction to Understanding the Catalytic Mechanism of Xanthosine Methyltransferase in Caffeine Biosynthesis from QM/MM Molecular Dynamics and Free Energy Simulations. 2280

Volume 56, Number 12, December 2016

Application Notes

• 
  Charly Empereur-mot, Jean-François Zagury, Matthieu Montès:
  Screening Explorer-An Interactive Tool for the Analysis of Screening Results. 2281-2286
• 
  Yu-Feng Lin, Chih-Wen Cheng, Chung-Shiuan Shih, Jenn-Kang Hwang, Chin-Sheng Yu, Chih-Hao Lu:
  MIB: Metal Ion-Binding Site Prediction and Docking Server. 2287-2291
• 
  Manish Sud:
  MayaChemTools: An Open Source Package for Computational Drug Discovery. 2292-2297

Perspectives

• 
  Mathew R. Koebel, Aaron Cooper, Grant Schmadeke, Soyoung Jeon, Mahesh Narayan, Suman Sirimulla:
  S···O and S···N Sulfur Bonding Interactions in Protein-Ligand Complexes: Empirical Considerations and Scoring Function. 2298-2309

Chemical Information

• 
  Dheivya Thiagarajan, Dinesh P. Mehta:
  Faster Algorithms for Isomer Network Generation. 2310-2319
• 
  Tomasz Fraczek:
  Simulation-Based Algorithm for Two-Dimensional Chemical Structure Diagram Generation of Complex Molecules and Ligand-Protein Interactions. 2320-2335
• 
  Nadine Schneider, Nikolaus Stiefl, Gregory A. Landrum:
  What's What: The (Nearly) Definitive Guide to Reaction Role Assignment. 2336-2346
• 
  Jerome G. P. Wicker, Richard I. Cooper:
  Beyond Rotatable Bond Counts: Capturing 3D Conformational Flexibility in a Single Descriptor. 2347-2352
• 
  Robert P. Sheridan, Wei Min Wang, Andy Liaw, Junshui Ma, Eric M. Gifford:
  Extreme Gradient Boosting as a Method for Quantitative Structure-Activity Relationships. 2353-2360

Computational Chemistry

• 
  Johannes G. E. M. Fraaije, Jan van Male, Paul Becherer, Rubèn Serral Gracià:
  Coarse-Grained Models for Automated Fragmentation and Parametrization of Molecular Databases. 2361-2377
• 
  Matthew D. King, Thomas Long, Timothy L. Andersen, Owen M. McDougal:
  Genetic Algorithm Managed Peptide Mutant Screening: Optimizing Peptide Ligands for Targeted Receptor Binding. 2378-2387
• 
  Daniel Cappel, Michelle Lynn Hall, Eelke B. Lenselink, Thijs Beuming, Jun Qi, James Bradner, Woody Sherman:
  Relative Binding Free Energy Calculations Applied to Protein Homology Models. 2388-2400
• 
  Rajendran Senthilkumar, Parthiban Marimuthu, Preethy Paul, Yesaiyan Manojkumar, Sankaralingam Arunachalam, John E. Eriksson, Mark S. Johnson:
  Plasma Protein Binding of Anisomelic Acid: Spectroscopy and Molecular Dynamic Simulations. 2401-2412
• 
  Xi Jiang, Ashutosh Kumar, Tian Liu, Kam Y. J. Zhang, Qing Yang:
  A Novel Scaffold for Developing Specific or Broad-Spectrum Chitinase Inhibitors. 2413-2420

Computational Biochemistry

• 
  Jingheng Wu, Sixiang Wen, Yiwei Zhou, Hui Chao, Yong Shen:
  Human Ferrochelatase: Insights for the Mechanism of Ferrous Iron Approaching Protoporphyrin IX by QM/MM and QTCP Free Energy Studies. 2421-2433
• 
  Petra Cechová, Karel Berka, Martin Kubala:
  Ion Pathways in the Na⁺/K⁺-ATPase. 2434-2444
• 
  Mitsugu Araki, Narutoshi Kamiya, Miwa Sato, Masahiko Nakatsui, Takatsugu Hirokawa, Yasushi Okuno:
  The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors. 2445-2456
• 
  Jakub Jakowiecki, Slawomir Filipek:
  Hydrophobic Ligand Entry and Exit Pathways of the CB1 Cannabinoid Receptor. 2457-2466
• 
  Balasubramanian Chandramouli, Giovanni Chillemi:
  Conformational Dynamics of Lysine Methyltransferase Smyd2. Insights into the Different Substrate Crevice Characteristics of Smyd2 and Smyd3. 2467-2475

Pharmaceutical Modeling

• 
  Arijit Basu, Yang-Sung Sohn, Mohamed Alyan, Rachel Nechushtai, Abraham J. Domb, Amiram Goldblum:
  Discovering Novel and Diverse Iron-Chelators in Silico. 2476-2485
• 
  Rajni K. Sharma, Marlene Espinoza-Moraga, Horacio Poblete, Ross G. Douglas, Edward D. Sturrock, Julio Caballero, Kelly Chibale:
  The Dynamic Nonprime Binding of Sampatrilat to the C-Domain of Angiotensin-Converting Enzyme. 2486-2494

Bioinformatics

• 
  Janaina Cruz Pereira, Ernesto Raúl Caffarena, Cícero Nogueira dos Santos:
  Boosting Docking-Based Virtual Screening with Deep Learning. 2495-2506
• 
  Naman Paul, Lavinia A. Carabet, Nada Lallous, Takeshi Yamazaki, Martin E. Gleave, Paul S. Rennie, Artem Cherkasov:
  Cheminformatics Modeling of Adverse Drug Responses by Clinically Relevant Mutants of Human Androgen Receptor. 2507-2516