Journal of Chemical Information and Modeling, Volume 55

Volume 55, Number 1, January 2015

Chemical Information

• 
  Obdulia Rabal, Fares Ibrahim Amr, Julen Oyarzabal:
  Novel Scaffold Fingerprint (SFP): Applications in Scaffold Hopping and Scaffold-Based Selection of Diverse Compounds. 1-18
• 
  Behrooz Torabi Moghadam, Jonathan Alvarsson, Marcus Holm, Martin Eklund, Lars Carlsson, Ola Spjuth:
  Scaling Predictive Modeling in Drug Development with Cloud Computing. 19-25
• 
  Tiago B. Oliveira, Leonardo Gobbo-Neto, Thomas J. Schmidt, Fernando B. Da Costa:
  Study of Chromatographic Retention of Natural Terpenoids by Chemoinformatic Tools. 26-38
• 
  Nadine Schneider, Daniel M. Lowe, Roger A. Sayle, Gregory A. Landrum:
  Development of a Novel Fingerprint for Chemical Reactions and Its Application to Large-Scale Reaction Classification and Similarity. 39-53

Computational Chemistry

• 
  Lukas Daniel, Tomas Buryska, Zbynek Prokop, Jirí Damborský, Jan Brezovsky:
  Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases Using in Silico Screening. 54-62
• 
  Denis Fourches, Regina Politi, Alexander Tropsha:
  Target-Specific Native/Decoy Pose Classifier Improves the Accuracy of Ligand Ranking in the CSAR 2013 Benchmark. 63-71
• 
  Carlos H. B. da Cruz, Gustavo de M. Seabra:
  QM/MM Simulations of Amyloid-β 42 Degradation by IDE in the Presence and Absence of ATP. 72-83
• 
  Héléna A. Gaspar, Igor I. Baskin, Gilles Marcou, Dragos Horvath, Alexandre Varnek:
  Chemical Data Visualization and Analysis with Incremental Generative Topographic Mapping: Big Data Challenge. 84-94
• 
  M. Álvarez-Moreno, Coen de Graaf, N. López, Feliu Maseras, Josep M. Poblet, Carles Bo:
  Managing the Computational Chemistry Big Data Problem: The ioChem-BD Platform. 95-103

Computational Biochemistry

• 
  Chunyan He, Jingfei Chen, Liaoyuan An, Yefei Wang, Zhiyu Shu, Lishan Yao:
  Carboxyl-Peptide Plane Stacking Is Important for Stabilization of Buried E305 of Trichoderma reesei Cel5A. 104-113
• 
  Sergey A. Samsonov, Leon Bichmann, M. Teresa Pisabarro:
  Coarse-Grained Model of Glycosaminoglycans. 114-124

Pharmaceutical Modeling

• 
  Mark C. Wenlock, Lars A. Carlsson:
  How Experimental Errors Influence Drug Metabolism and Pharmacokinetic QSAR/QSPR Models. 125-134
• 
  José L. Domínguez, Fernando Fernández-Nieto, Marian Castro, Marco Catto, M. Rita Paleo, Silvia Porto, Francisco Javier Sardina, José M. Brea, Angelo Carotti, M. Carmen Villaverde, Fredy Sussman:
  Computer-Aided Structure-Based Design of Multitarget Leads for Alzheimer's Disease. 135-148
• 
  Jiansong Fang, Yongjie Li, Rui Liu, Xiaocong Pang, Chao Li, Ranyao Yang, Yangyang He, Wenwen Lian, Ailin Liu, Guanhua Du:
  Discovery of Multitarget-Directed Ligands against Alzheimer's Disease through Systematic Prediction of Chemical-Protein Interactions. 149-164
• 
  Timo Krotzky, Christian Grunwald, Ute Egerland, Gerhard Klebe:
  Large-Scale Mining for Similar Protein Binding Pockets: With RAPMAD Retrieval on the Fly Becomes Real. 165-179
• 
  Bernard Pirard, Peter Ertl:
  Evaluation of a Semi-Automated Workflow for Fragment Growing. 180-193
• 
  Vijay M. Khedkar, Evans C. Coutinho:
  CoRILISA: A Local Similarity Based Receptor Dependent QSAR Method. 194-205

Errata

• 
  Catarina A. Carvalheda, Sara R. R. Campos, Miguel Machuqueiro, António M. Baptista:
  Correction to "Structural Effects of pH and Deacylation on Surfactant Protein C in an Organic Solvent Mixture: A Constant-pH MD Study". 206

Volume 55, Number 2, February 2015

Chemical Information

• 
  Julia Weber, Janosch Achenbach, Daniel Moser, Ewgenij Proschak:
  VAMMPIRE-LORD: A Web Server for Straightforward Lead Optimization Using Matched Molecular Pairs. 207-213
• 
  John D. Holliday, Nor Sani, Peter Willett:
  Calculation of Substructural Analysis Weights Using a Genetic Algorithm. 214-221
• 
  Edmund Duesbury, John D. Holliday, Peter Willett:
  Maximum Common Substructure-Based Data Fusion in Similarity Searching. 222-230
• 
  Robert P. Sheridan, Daniel R. McMasters, Johannes H. Voigt, Mary Jo Wildey:
  eCounterscreening: Using QSAR Predictions to Prioritize Testing for Off-Target Activities and Setting the Balance between Benefit and Risk. 231-238
• 
  Gilles Marcou, João Aires-de-Sousa, Diogo A. R. S. Latino, Aurélie de Luca, Dragos Horvath, V. Rietsch, Alexandre Varnek:
  Expert System for Predicting Reaction Conditions: The Michael Reaction Case. 239-250
• 
  Oscar Méndez-Lucio, Albert J. Kooistra, Chris de Graaf, Andreas Bender, José L. Medina-Franco:
  Analyzing Multitarget Activity Landscapes Using Protein-Ligand Interaction Fingerprints: Interaction Cliffs. 251-262
• 
  Junshui Ma, Robert P. Sheridan, Andy Liaw, George E. Dahl, Vladimir Svetnik:
  Deep Neural Nets as a Method for Quantitative Structure-Activity Relationships. 263-274

Computational Chemistry

• 
  Tim ten Brink, Clementine Aguirre, Thomas E. Exner, Isabelle Krimm:
  Performance of Protein-Ligand Docking with Simulated Chemical Shift Perturbations. 275-283
• 
  Daniel Moser, Sandra K. Wittmann, Jan Kramer, René Blöcher, Janosch Achenbach, Denys Pogoryelov, Ewgenij Proschak:
  PENG: A Neural Gas-Based Approach for Pharmacophore Elucidation. Method Design, Validation, and Virtual Screening for Novel Ligands of LTA4H. 284-293
• 
  Barbara Zarzycka, Tom Seijkens, Sander B. Nabuurs, Tina Ritschel, Jochen Grommes, Oliver Soehnlein, Roy Schrijver, Claudia M. van Tiel, Tilman M. Hackeng, Christian Weber, Fabian Giehler, Arnd Kieser, Esther Lutgens, Gert Vriend, Gerry A. F. Nicolaes:
  Discovery of Small Molecule CD40-TRAF6 Inhibitors. 294-307

Computational Biochemistry

• 
  Nur Kusaira Khairul Ikram, Jacob D. Durrant, Muchtaridi Muchtaridi, Ayunni Salihah Zalaludin, Neny Purwitasari, Nornisah Mohamed, Aisyah Saad Abdul Rahim, Chan Kit Lam, Yahaya M. Normi, Noorsaadah Abdul Rahman, Rommie E. Amaro, Habibah A. Wahab:
  A Virtual Screening Approach For Identifying Plants with Anti H5N1 Neuraminidase Activity. 308-316
• 
  Wenjuan Huang, Nikolay Blinov, David S. Wishart, Andriy Kovalenko:
  Role of Water in Ligand Binding to Maltose-Binding Protein: Insight from a New Docking Protocol Based on the 3D-RISM-KH Molecular Theory of Solvation. 317-328
• 
  Chao Yang, Shilei Zhang, Ping He, Congcong Wang, Jian Huang, Peng Zhou:
  Self-Binding Peptides: Folding or Binding? 329-342
• 
  Martin Lindh, Fredrik Svensson, Wesley Schaal, Jin Zhang, Christian Sköld, Peter Brandt, Anders Karlén:
  Toward a Benchmarking Data Set Able to Evaluate Ligand- and Structure-based Virtual Screening Using Public HTS Data. 343-353
• 
  Lee Macomber, Mona S. Minkara, Robert P. Hausinger, Kenneth M. Merz Jr.:
  Reduction of Urease Activity by Interaction with the Flap Covering the Active Site. 354-361

Pharmaceutical Modeling

• 
  Khaled H. Barakat, Anwar Anwar-Mohamed, Jack A. Tuszynski, Morris J. Robins, D. Lorne Tyrrell, Michael Houghton:
  A Refined Model of the HCV NS5A Protein Bound to Daclatasvir Explains Drug-Resistant Mutations and Activity against Divergent Genotypes. 362-373
• 
  Jie Xia, Ermias Lemma Tilahun, Eyob Hailu Kebede, Terry-Elinor Reid, Liang Ren Zhang, Xiang Simon Wang:
  Comparative Modeling and Benchmarking Data Sets for Human Histone Deacetylases and Sirtuin Families. 374-388
• 
  Robert Fraczkiewicz, Mario Lobell, Andreas H. Göller, Ursula Krenz, Rolf Schoenneis, Robert D. Clark, Alexander Hillisch:
  Best of Both Worlds: Combining Pharma Data and State of the Art Modeling Technology To Improve in Silico pK_a Prediction. 389-397
• 
  Christoph Scholz, Sabine Knorr, Kay Hamacher, Boris Schmidt:
  DOCKTITE - A Highly Versatile Step-by-Step Workflow for Covalent Docking and Virtual Screening in the Molecular Operating Environment. 398-406
• 
  Wenbo Yu, Sirish Kaushik Lakkaraju, E. Prabhu Raman, Lei Fang, Alexander D. MacKerell Jr.:
  Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules. 407-420
• 
  Petar M. Mitrasinovic:
  Sequence-Dependent Binding of Flavonoids to Duplex DNA. 421-433
• 
  Bo-Han Su, Yi-shu Tu, Olivia A. Lin, Yeu-Chern Harn, Meng-yu Shen, Yufeng J. Tseng:
  Rule-Based Classification Models of Molecular Autofluorescence. 434-445

Bioinformatics

• 
  Hiroaki Iwata, Ryusuke Sawada, Sayaka Mizutani, Yoshihiro Yamanishi:
  Systematic Drug Repositioning for a Wide Range of Diseases with Integrative Analyses of Phenotypic and Molecular Data. 446-459

Software Description

• 
  Thomas Sander, Joël Freyss, Modest von Korff, Christian Rufener:
  DataWarrior: An Open-Source Program For Chemistry Aware Data Visualization And Analysis. 460-473

Errata

• 
  Nadine Schneider, Daniel M. Lowe, Roger A. Sayle, Gregory A. Landrum:
  Corrections to "Development of a Novel Fingerprint for Chemical Reactions and Its Application to Large-Scale Reaction Classification and Similarity". 474

Volume 55, Number 3, March 2015

Perspectives

• 
  Jie Liu, Renxiao Wang:
  Classification of Current Scoring Functions. 475-482
• 
  Christian Kramer, Julian E. Fuchs, Klaus R. Liedl:
  Strong Nonadditivity as a Key Structure-Activity Relationship Feature: Distinguishing Structural Changes from Assay Artifacts. 483-494

Letters

• 
  Jérémie Mortier, Elisabeth K. Nyakatura, Oliver Reimann, Susanne Huhmann, Jan O. Daldrop, Carsten Baldauf, Gerhard Wolber, Markus Miettinen, Beate Koksch:
  Coiled-Coils in Phage Display Screening: Insight into Exceptional Selectivity Provided by Molecular Dynamics. 495-500

Chemical Information

• 
  Aileen E. Day, Simon J. Coles, Colin L. Bird, Jeremy G. Frey, Richard J. Whitby, Valery Tkachenko, Antony J. Williams:
  ChemTrove: Enabling a Generic ELN To Support Chemistry through the Use of Transferable Plug-ins and Online Data Sources. 501-509
• 
  Chihae Yang, Aleksey Tarkhov, Jörg Marusczyk, Bruno Bienfait, Johann Gasteiger, Thomas Kleinöder, Tomasz Magdziarz, Oliver Sacher, Christof H. Schwab, Johannes Schwöbel, Lothar Terfloth, Kirk Arvidson, Ann Richard, Andrew P. Worth, James Rathman:
  New Publicly Available Chemical Query Language, CSRML, To Support Chemotype Representations for Application to Data Mining and Modeling. 510-528
• 
  Chetan Rupakheti, Aaron Virshup, Weitao Yang, David N. Beratan:
  Strategy To Discover Diverse Optimal Molecules in the Small Molecule Universe. 529-537

Computational Chemistry

• 
  Andrea Volkamer, Sameh Eid, Samo Turk, Sabrina Jaeger, Friedrich Rippmann, Simone Fulle:
  Pocketome of Human Kinases: Prioritizing the ATP Binding Sites of (Yet) Untapped Protein Kinases for Drug Discovery. 538-549
• 
  David Rodríguez, Zhang-Guo Gao, Steven M. Moss, Kenneth A. Jacobson, Jens Carlsson:
  Molecular Docking Screening Using Agonist-Bound GPCR Structures: Probing the A_2A Adenosine Receptor. 550-563
• 
  Danny E. P. Vanpoucke, Julianna Oláh, Frank De Proft, Veronique Van Speybroeck, Goedele Roos:
  Convergence of Atomic Charges with the Size of the Enzymatic Environment. 564-571
• 
  Zhiwei Feng, Larry V. Pearce, Xiaomeng Xu, Xiaole Yang, Peng Yang, Peter M. Blumberg, Xiang-Qun Xie:
  Structural Insight into Tetrameric hTRPV1 from Homology Modeling, Molecular Docking, Molecular Dynamics Simulation, Virtual Screening, and Bioassay Validations. 572-588
• 
  Luigi Capoferri, Alessio Lodola, Silvia Rivara, Marco Mor:
  Quantum Mechanics/Molecular Mechanics Modeling of Covalent Addition between EGFR-Cysteine 797 and N-(4-Anilinoquinazolin-6-yl) Acrylamide. 589-599

Computational Biochemistry

• 
  Fergal J. Duffy, Darragh O'Donovan, Marc Devocelle, Niamh Moran, David J. O'Connell, Denis C. Shields:
  Virtual Screening Using Combinatorial Cyclic Peptide Libraries Reveals Protein Interfaces Readily Targetable by Cyclic Peptides. 600-613
• 
  Quanjie Li, Soo-Kyung Kim, William A. Goddard III, Guangju Chen, Hongwei Tan:
  Predicted Structures for Kappa Opioid G-Protein Coupled Receptor Bound to Selective Agonists. 614-627
• 
  Veronika Navrátilová, Markéta Paloncýová, Michaela Kajsová, Karel Berka, Michal Otyepka:
  Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4. 628-635
• 
  Caterina Bianchi, Ronen Zangi:
  Molecular Dynamics Study of the Recognition of Dimethylated CpG Sites by MBD1 Protein. 636-644
• 
  Alexander L. Perryman, Weixuan Yu, Xin Wang, Sean Ekins, Stefano Forli, Shao-Gang Li, Joel S. Freundlich, Peter J. Tonge, Arthur J. Olson:
  A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of Mycobacterium tuberculosis InhA. 645-659

Pharmaceutical Modeling

• 
  Rasmus Leth, Patrik Rydberg, Flemming Steen Jørgensen, Lars Olsen:
  Density Functional Theory Study on the Formation of Reactive Benzoquinone Imines by Hydrogen Abstraction. 660-666
• 
  Giulio Poli, Niccolò Giuntini, Adriano Martinelli, Tiziano Tuccinardi:
  Application of a FLAP-Consensus Docking Mixed Strategy for the Identification of New Fatty Acid Amide Hydrolase Inhibitors. 667-675
• 
  Andrew Anighoro, Dagmar Stumpfe, Kathrin Heikamp, Kristin Beebe, Leonard M. Neckers, Jürgen Bajorath, Giulio Rastelli:
  Computational Polypharmacology Analysis of the Heat Shock Protein 90 Interactome. 676-686
• 
  Markus O. Zimmermann, Andreas Lange, Frank M. Boeckler:
  Evaluating the Potential of Halogen Bonding in Molecular Design: Automated Scaffold Decoration Using the New Scoring Function XBScore. 687-699
• 
  Sirish Kaushik Lakkaraju, Wenbo Yu, E. Prabhu Raman, Alena V. Hershfeld, Lei Fang, Deepak Deshpande, Alexander D. MacKerell Jr.:
  Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors. 700-708

Bioinformatics

• 
  Mai Hamdalla, Sanguthevar Rajasekaran, David F. Grant, Ion I. Mandoiu:
  Metabolic Pathway Predictions for Metabolomics: A Molecular Structure Matching Approach. 709-718

Volume 55, Number 4, April 2015

Editorial

• 
  Kenneth M. Merz Jr., Matthias Rarey, Alexander Tropsha, Habibah A. Wahab:
  Letter from the Editors. 719-720

Application Notes

• 
  Demian Riccardi, Jerry M. Parks, Alexander Johs, Jeremy C. Smith:
  HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales. 721-726

Computational Chemistry

• 
  Shuai Liu, Lingle Wang, David L. Mobley:
  Is Ring Breaking Feasible in Relative Binding Free Energy Calculations? 727-735
• 
  Xiang-Wei Zhu, Yan-Jun Xin, Hui-Lin Ge:
  Recursive Random Forests Enable Better Predictive Performance and Model Interpretation than Variable Selection by LASSO. 736-746

Computational Biochemistry

• 
  Nan Liu, Jeffrey R. Van Voorst, John B. Johnston, Leslie A. Kuhn:
  CholMine: Determinants and Prediction of Cholesterol and Cholate Binding Across Nonhomologous Protein Structures. 747-759
• 
  Anju C. Pushkaran, Namrata Nataraj, Nisha Nair, Friedrich Götz, Raja Biswas, C. Gopi Mohan:
  Understanding the Structure-Function Relationship of Lysozyme Resistance in Staphylococcus aureus by Peptidoglycan O-Acetylation Using Molecular Docking, Dynamics, and Lysis Assay. 760-770
• 
  Eva Nittinger, Nadine Schneider, Gudrun Lange, Matthias Rarey:
  Evidence of Water Molecules - A Statistical Evaluation of Water Molecules Based on Electron Density. 771-783
• 
  Hua Wan, Shan Chang, Jianping Hu, Yuan-xin Tian, Xu-hong Tian:
  Molecular Dynamics Simulations of Ternary Complexes: Comparisons of LEAFY Protein Binding to Different DNA Motifs. 784-794
• 
  Bruno L. Victor, Diana Lousa, Jorge M. Antunes, Cláudio M. Soares:
  Self-Assembly Molecular Dynamics Simulations Shed Light into the Interaction of the Influenza Fusion Peptide with a Membrane Bilayer. 795-805
• 
  Amanda E. Wakefield, William M. Wuest, Vincent A. Voelz:
  Molecular Simulation of Conformational Pre-Organization in Cyclic RGD Peptides. 806-813
• 
  Tobias Linder, Shizhen Wang, Eva-Maria Zangerl-Plessl, Colin G. Nichols, Anna Stary-Weinzinger:
  Molecular Dynamics Simulations of KirBac1.1 Mutants Reveal Global Gating Changes of Kir Channels. 814-822

Pharmaceutical Modeling

• 
  Sabina Smusz, Stefan Mordalski, Jagna Witek, Krzysztof Rataj, Rafal Kafel, Andrzej J. Bojarski:
  Multi-Step Protocol for Automatic Evaluation of Docking Results Based on Machine Learning Methods - A Case Study of Serotonin Receptors 5-HT₆ and 5-HT₇. 823-832
• 
  Fang Bai, Sha Liao, Junfeng Gu, Hualiang Jiang, Xicheng Wang, Honglin Li:
  An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy. 833-847
• 
  Chinmayee Choudhury, U. Deva Priyakumar, G. Narahari Sastry:
  Dynamics Based Pharmacophore Models for Screening Potential Inhibitors of Mycobacterial Cyclopropane Synthase. 848-860
• 
  Xuben Hou, Jintong Du, Renshuai Liu, Yi Zhou, Minyong Li, Wenfang Xu, Hao Fang:
  Enhancing the Sensitivity of Pharmacophore-Based Virtual Screening by Incorporating Customized ZBG Features: A Case Study Using Histone Deacetylase 8. 861-871

Bioinformatics

• 
  Mohammad Moghadasi, Hanieh Mirzaei, Artem B. Mamonov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis, Dima Kozakov:
  The Impact of Side-Chain Packing on Protein Docking Refinement. 872-881
• 
  Alexandre Borrel, Leslie Regad, Henri Xhaard, Michel Petitjean, Anne-Claude Camproux:
  PockDrug: A Model for Predicting Pocket Druggability That Overcomes Pocket Estimation Uncertainties. 882-895

Software Description

• 
  Nikolaus Stiefl, Peter Gedeck, Donovan Chin, Peter Hunt, Mika K. Lindvall, Katrin Spiegel, Clayton Springer, Scott Biller, Christoph L. Buenemann, Takanori Kanazawa, Mitsunori Kato, Richard A. Lewis, Eric J. Martin, Valery R. Polyakov, Ruben Tommasi, John H. Van Drie, Brian Vash, Lewis Whitehead, Yongjin Xu, Ruben Abagyan, Eugene Raush, Maxim Totrov:
  FOCUS - Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists. 896-908

Volume 55, Number 5, May 2015

Application Notes

• 
  Matt J. Harvey, Gianni De Fabritiis:
  AceCloud: Molecular Dynamics Simulations in the Cloud. 909-914

Chemical Information

• 
  Xavier Lucas, Björn A. Grüning, Stefan Bleher, Stefan Günther:
  The Purchasable Chemical Space: A Detailed Picture. 915-924
• 
  Jean-Philippe Métivier, Alban Lepailleur, Aleksey Buzmakov, Guillaume Poezevara, Bruno Crémilleux, Sergei O. Kuznetsov, Jérémie Le Goff, Amedeo Napoli, Ronan Bureau, Bertrand Cuissart:
  Discovering Structural Alerts for Mutagenicity Using Stable Emerging Molecular Patterns. 925-940
• 
  Péter Englert, Péter Kovács:
  Efficient Heuristics for Maximum Common Substructure Search. 941-955
• 
  Mateusz Maciejewski, Anne Mai Wassermann, Meir Glick, Eugen Lounkine:
  Experimental Design Strategy: Weak Reinforcement Leads to Increased Hit Rates and Enhanced Chemical Diversity. 956-962
• 
  Ankita Garg, Catherine G. Enright, Michael G. Madden:
  Improving Spectral Library Search by Redefining Similarity Measures. 963-971

Computational Chemistry

• 
  Jed Zaretzki, Kevin Michael Boehm, Sanjay Joshua Swamidass:
  Improved Prediction of CYP-Mediated Metabolism with Chemical Fingerprints. 972-982
• 
  Andreas Truszkowski, Karina van den Broek, Hubert Kuhn, Achim Zielesny, Matthias Epple:
  Mesoscopic Simulation of Phospholipid Membranes, Peptides, and Proteins with Molecular Fragment Dynamics. 983-997
• 
  Xiliang Yan, Jianfen Fan, Yi Yu, Jian Xu, Mingming Zhang:
  Transport Behavior of a Single Ca²⁺, K⁺, and Na⁺ in a Water-Filled Transmembrane Cyclic Peptide Nanotube. 998-1011
• 
  Qiyao Zhang, Longjiu Cheng:
  Structural Determination of (Al₂O₃)_n (n = 1-15) Clusters Based on Graphic Processing Unit. 1012-1020

Computational Biochemistry

• 
  Wei Ye, Dingjue Ji, Wei Wang, Ray Luo, Hai-Feng Chen:
  Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins. 1021-1029

Pharmaceutical Modeling

• 
  Sabine Schultes, Albert J. Kooistra, Henry F. Vischer, Saskia Nijmeijer, Eric E. J. Haaksma, Rob Leurs, Iwan J. P. de Esch, Chris de Graaf:
  Combinatorial Consensus Scoring for Ligand-Based Virtual Fragment Screening: A Comparative Case Study for Serotonin 5-HT₃A, Histamine H₁, and Histamine H₄ Receptors. 1030-1044
• 
  Albert J. Kooistra, Rob Leurs, Iwan J. P. de Esch, Chris de Graaf:
  Structure-Based Prediction of G-Protein-Coupled Receptor Ligand Function: A β-Adrenoceptor Case Study. 1045-1061
• 
  Jarmila Husby, Giovanni Bottegoni, Irina Kufareva, Ruben Abagyan, Andrea Cavalli:
  Structure-Based Predictions of Activity Cliffs. 1062-1076

Software Description

• 
  Cristian R. Munteanu, António César Pimenta, Carlos Fernandez-Lozano, André Melo, M. N. D. S. Cordeiro, Irina S. Moreira:
  Solvent Accessible Surface Area-Based Hot-Spot Detection Methods for Protein-Protein and Protein-Nucleic Acid Interfaces. 1077-1086

Volume 55, Number 6, June 2015

Editorial

• 
  Markus Wagener, Frank Oellien, Uli Fechner, Matthias Rarey:
  10th ICCS/GCC Conference: 40 Years of Cheminformatics. 1087

Chemical Information

• 
  Stanislav Geidl, Radka Svobodová Vareková, Veronika Bendová, Lukás Petrusek, Crina-Maria Ionescu, Zdenek Jurka, Ruben Abagyan, Jaroslav Koca:
  How Does the Methodology of 3D Structure Preparation Influence the Quality of pK_a Prediction? 1088-1097
• 
  Robert P. Sheridan:
  The Relative Importance of Domain Applicability Metrics for Estimating Prediction Errors in QSAR Varies with Training Set Diversity. 1098-1107
• 
  Tatsuya Okuno, Koya Kato, Tomoki P. Terada, Masaki Sasai, George Chikenji:
  VS-APPLE: A Virtual Screening Algorithm Using Promiscuous Protein-Ligand Complexes. 1108-1119
• 
  Nidhi Singh, Sameer Tiwari, Kishore K. Srivastava, Mohammad Imran Siddiqi:
  Identification of Novel Inhibitors of Mycobacterium tuberculosis PknG Using Pharmacophore Based Virtual Screening, Docking, Molecular Dynamics Simulation, and Their Biological Evaluation. 1120-1129
• 
  Sriram Tyagarajan, Christopher T. Lowden, Zhengwei Peng, Kevin D. Dykstra, Edward C. Sherer, Shane W. Krska:
  Heterocyclic Regioisomer Enumeration (HREMS): A Cheminformatics Design Tool. 1130-1135
• 
  Jenny Balfer, Jürgen Bajorath:
  Visualization and Interpretation of Support Vector Machine Activity Predictions. 1136-1147

Computational Chemistry

• 
  Aneta Jezierska, Jaroslaw J. Panek:
  "Zwitterionic Proton Sponge" Hydrogen Bonding Investigations on the Basis of Car-Parrinello Molecular Dynamics. 1148-1157
• 
  Randy Jalem, Mayumi Kimura, Masanobu Nakayama, Toshihiro Kasuga:
  Informatics-Aided Density Functional Theory Study on the Li Ion Transport of Tavorite-Type LiMTO₄F (M³⁺-T⁵⁺, M²⁺-T⁶⁺). 1158-1168
• 
  Nicholas C. Firth, Butrus Atrash, Nathan Brown, Julian Blagg:
  MOARF, an Integrated Workflow for Multiobjective Optimization: Implementation, Synthesis, and Biological Evaluation. 1169-1180
• 
  Samuel R. Perry, Weijun Xu, Anna Wirija, Junxian Lim, Mei-Kwan Yau, Martin J. Stoermer, Andrew J. Lucke, David P. Fairlie:
  Three Homology Models of PAR2 Derived from Different Templates: Application to Antagonist Discovery. 1181-1191
• 
  Jin Zhang, Badamkhatan Tuguldur, David van der Spoel:
  Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation. 1192-1201

Computational Biochemistry

• 
  Nandhitha Subramanian, Karmen Condic-Jurkic, Alan E. Mark, Megan L. O'Mara:
  Identification of Possible Binding Sites for Morphine and Nicardipine on the Multidrug Transporter P-Glycoprotein Using Umbrella Sampling Techniques. 1202-1217
• 
  Liang Xu, Shengsheng Shan, Yonggang Chen, Xiaojuan Wang, Ruth Nussinov, Buyong Ma:
  Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Aβ40 Peptide Oligomerization. 1218-1230

Pharmaceutical Modeling

• 
  Alex M. Clark, Krishna Dole, Anna Coulon-Spektor, Andrew M. McNutt, George Grass, Joel S. Freundlich, Robert C. Reynolds, Sean Ekins:
  Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets. 1231-1245
• 
  Alex M. Clark, Sean Ekins:
  Open Source Bayesian Models. 2. Mining a "Big Dataset" To Create and Validate Models with ChEMBL. 1246-1260

Bioinformatics

• 
  Jia-Feng Yu, Xianghua Dou, Hong-Bo Wang, Xiao Sun, Huiying Zhao, Ji-Hua Wang:
  A Novel Cylindrical Representation for Characterizing Intrinsic Properties of Protein Sequences. 1261-1270
• 
  Pawel Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Cezary Czaplewski, Adam Liwo:
  Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field. 1271-1281

Software Description

• 
  Marco Foscato, Robert J. Deeth, Vidar R. Jensen:
  Integration of Ligand Field Molecular Mechanics in Tinker. 1282-1290

Volume 55, Number 7, July 2015

Editorial

• 
  Kenneth M. Merz Jr.:
  Introducing the Review Manuscript Type. 1291

Application Notes

• 
  Sirus Saeedipour, David Tai, Jianwen Fang:
  ChemCom: A Software Program for Searching and Comparing Chemical Libraries. 1292-1296

Perspectives

• 
  Nathalie Lagarde, Jean-François Zagury, Matthieu Montès:
  Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives. 1297-1307

Chemical Information

• 
  Qing-You Zhang, Chengcheng Wu, Fangfang Zheng, Tanfeng Zhao, Yanmei Zhou, Lu Xu:
  Extension of a Highly Discriminating Topological Index. 1308-1315
• 
  David L. J. Alexander, Alexander Tropsha, David A. Winkler:
  Beware of R²: Simple, Unambiguous Assessment of the Prediction Accuracy of QSAR and QSPR Models. 1316-1322

Computational Chemistry

• 
  Francis Gaudreault, Rafael J. Najmanovich:
  FlexAID: Revisiting Docking on Non-Native-Complex Structures. 1323-1336
• 
  Nikita Basant, Shikha Gupta, Kunwar P. Singh:
  Predicting Toxicities of Diverse Chemical Pesticides in Multiple Avian Species Using Tree-Based QSAR Approaches for Regulatory Purposes. 1337-1348
• 
  Gerald Zapata-Torres, Angelica Fierro, German Barriga-González, J. Cristian Salgado, Cristian Celis-Barros:
  Revealing Monoamine Oxidase B Catalytic Mechanisms by Means of the Quantum Chemical Cluster Approach. 1349-1360

Computational Biochemistry

• 
  Fangqiang Zhu, Bo Chen:
  Monte Carlo Simulations of HIV Capsid Protein Homodimer. 1361-1368
• 
  Xiangfei Song, Yefei Wang, Shujun Zhang, Shihai Yan, Tong Li, Lishan Yao:
  Characterization of the Dielectric Constant in the Trichoderma reesei Cel7B Active Site. 1369-1376
• 
  Antonella Paladino, Giulia Morra, Giorgio Colombo:
  Structural Stability and Flexibility Direct the Selection of Activating Mutations in Epidermal Growth Factor Receptor Kinase. 1377-1387

Pharmaceutical Modeling

• 
  Olga A. Tarasova, Aleksandra F. Urusova, Dmitry Filimonov, Marc C. Nicklaus, Alexey V. Zakharov, Vladimir Poroikov:
  QSAR Modeling Using Large-Scale Databases: Case Study for HIV-1 Reverse Transcriptase Inhibitors. 1388-1399
• 
  Nan Li, Richard I. Ainsworth, Bo Ding, Tingjun Hou, Wei Wang:
  Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease. 1400-1412
• 
  Isidro Cortes-Ciriano, Andreas Bender, Thérèse E. Malliavin:
  Comparing the Influence of Simulated Experimental Errors on 12 Machine Learning Algorithms in Bioactivity Modeling Using 12 Diverse Data Sets. 1413-1425
• 
  Bo-Han Su, Yi-shu Tu, Chieh Lin, Chi-Yu Shao, Olivia A. Lin, Yufeng J. Tseng:
  Rule-Based Prediction Models of Cytochrome P450 Inhibition. 1426-1434
• 
  Anders Poulsen, Soo Yei Ho, Weiling Wang, Jenefer Alam, Duraiswamy A. Jeyaraj, Shi Hua Ang, Eldwin Sum Wai Tan, Grace Ruiting Lin, Vivien Wei Wen Cheong, Zhiyuan Ke, May Ann Lee, Thomas H. Keller:
  Pharmacophore Model for Wnt/Porcupine Inhibitors and Its Use in Drug Design. 1435-1448
• 
  Peter Gedeck, Yipin Lu, Suzanne Skolnik, Stephane Rodde, Gavin Dollinger, Weiping Jia, Giuliano Berellini, Riccardo Vianello, Bernard Faller, Franco Lombardo:
  Benefit of Retraining pK_a Models Studied Using Internally Measured Data. 1449-1459
• 
  Cen Gao, Nels Thorsteinson, Ian A. Watson, Ji-Bo Wang, Michal Vieth:
  Knowledge-Based Strategy to Improve Ligand Pose Prediction Accuracy for Lead Optimization. 1460-1468

Bioinformatics

• 
  Indrajit Saha, Benedykt Rak, Shib Sankar Bhowmick, Ujjwal Maulik, Debotosh Bhattacharjee, Uwe Koch, Michal Lazniewski, Dariusz Plewczynski:
  Binding Activity Prediction of Cyclin-Dependent Inhibitors. 1469-1482
• 
  Tianyun Liu, Russ B. Altman:
  Relating Essential Proteins to Drug Side-Effects Using Canonical Component Analysis: A Structure-Based Approach. 1483-1494
• 
  Florian Krull, Gerrit Korff, Nadia Elghobashi-Meinhardt, Ernst-Walter Knapp:
  ProPairs: A Data Set for Protein-Protein Docking. 1495-1507

Errata

• 
  Alexandra T. P. Carvalho, Marcel Swart:
  Correction for Electronic Structure Investigation and Parametrization of Biologically Relevant Iron-Sulfur Clusters. 1508

Volume 55, Number 8, August 2015

Application Notes

• 
  Mahendra Awale, Jean-Louis Reymond:
  Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces. 1509-1516
• 
  Karen Sargsyan, Yun Hao Hua, Carmay Lim:
  Clustangles: An Open Library for Clustering Angular Data. 1517-1520

Chemical Information

• 
  Samo Lesnik, Tanja Stular, Boris Brus, Damijan Knez, Stanislav Gobec, Dusanka Janezic, Janez Konc:
  LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors. 1521-1528
• 
  Frank R. Burden, David A. Winkler:
  Relevance Vector Machines: Sparse Classification Methods for QSAR. 1529-1534
• 
  Stefan Bietz, Karen T. Schomburg, Matthias Hilbig, Matthias Rarey:
  Discriminative Chemical Patterns: Automatic and Interactive Design. 1535-1546
• 
  M. Elstner, A. Schiller:
  Playing Tic-Tac-Toe with a Sugar-Based Molecular Computer. 1547-1551

Computational Chemistry

• 
  Alexander S. Bayden, Demetri T. Moustakas, Diane Joseph-McCarthy, Michelle L. Lamb:
  Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP. 1552-1565
• 
  Ruifeng Liu, Patric Schyman, Anders Wallqvist:
  Critically Assessing the Predictive Power of QSAR Models for Human Liver Microsomal Stability. 1566-1575
• 
  Denis Sh. Sabirov, Eiji Osawa:
  Information Entropy of Fullerenes. 1576-1584

Computational Biochemistry

• 
  David Rooklin, Cheng Wang, Joseph Katigbak, Paramjit S. Arora, Yingkai Zhang:
  AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein-Protein Interaction Interfaces. 1585-1599
• 
  Matthieu Chartier, Rafael Najmanovich:
  Detection of Binding Site Molecular Interaction Field Similarities. 1600-1615
• 
  Peng Lian, LinLang Li, Chuanrong Geng, Xuechu Zhen, Wei Fu:
  Higher-Affinity Agonists of 5-HT_1AR Discovered through Tuning the Binding-Site Flexibility. 1616-1627
• 
  Mingzhen Zhang, Rundong Hu, Hong Chen, Xiong Gong, Feimeng Zhou, Li Zhang, Jie Zheng:
  Polymorphic Associations and Structures of the Cross-Seeding of Aβ_1-42 and hIAPP_1-37 Polypeptides. 1628-1639
• 
  Ignacio Lizana, Gonzalo A. Jaña, Eduardo J. Delgado:
  New Insights on the Reaction Pathway Leading to Lactyl-ThDP: A Theoretical Approach. 1640-1644
• 
  Amanda Tse, Gennady M. Verkhivker:
  Molecular Dynamics Simulations and Structural Network Analysis of c-Abl and c-Src Kinase Core Proteins: Capturing Allosteric Mechanisms and Communication Pathways from Residue Centrality. 1645-1662
• 
  Weizhuang Zhou, Grace W. Tang, Russ B. Altman:
  High Resolution Prediction of Calcium-Binding Sites in 3D Protein Structures Using FEATURE. 1663-1672

Pharmaceutical Modeling

• 
  Fei Qi, Satoshi Fudo, Saburo Neya, Tyuji Hoshino:
  A Dominant Factor for Structural Classification of Protein Crystals. 1673-1685
• 
  Arumugam Ramachandran Muralidharan, Chandrabose Selvaraj, Sanjeev Kumar Singh, Joen-Rong Sheu, Philip A. Thomas, Pitchairaj Geraldine:
  Structure-Based Virtual Screening and Biological Evaluation of a Calpain Inhibitor for Prevention of Selenite-Induced Cataractogenesis in an in Vitro System. 1686-1697
• 
  María Herrero-Zazo, Isabel Segura-Bedmar, Janna Hastings, Paloma Martínez:
  DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug-Drug Interactions and Their Mechanisms. 1698-1707
• 
  Saroj Verma, Utsab Debnath, Pooja Agarwal, Kumkum Srivastava, Yenamandra S. Prabhakar:
  In Silico Exploration for New Antimalarials: Arylsulfonyloxy Acetimidamides as Prospective Agents. 1708-1719
• 
  Helen Ha, Bikash Debnath, Srinivas Odde, Tim Bensman, Henry Ho, Paul M. Beringer, Nouri Neamati:
  Discovery of Novel CXCR2 Inhibitors Using Ligand-Based Pharmacophore Models. 1720-1738
• 
  Fabian P. Steinmetz, Judith C. Madden, Mark T. D. Cronin:
  Data Quality in the Human and Environmental Health Sciences: Using Statistical Confidence Scoring to Improve QSAR/QSPR Modeling. 1739-1746

Bioinformatics

• 
  Stefan Bietz, Matthias Rarey:
  ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations. 1747-1756
• 
  Ambrish Roy, Bharath Srinivasan, Jeffrey Skolnick:
  PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity. 1757-1770

Software Description

• 
  Brian P. Kelley, Scott P. Brown, Gregory L. Warren, Steven W. Muchmore:
  POSIT: Flexible Shape-Guided Docking For Pose Prediction. 1771-1780

Volume 55, Number 9, September 2015

Perspectives

• 
  Eleanor J. Gardiner, Valerie J. Gillet:
  Perspectives on Knowledge Discovery Algorithms Recently Introduced in Chemoinformatics: Rough Set Theory, Association Rule Mining, Emerging Patterns, and Formal Concept Analysis. 1781-1803

Chemical Information

• 
  Violeta I. Pérez-Nueno, Michel Souchet, Arnaud Sinan Karaboga, David W. Ritchie:
  GESSE: Predicting Drug Side Effects from Drug-Target Relationships. 1804-1823
• 
  Florent Chevillard, Peter Kolb:
  SCUBIDOO: A Large yet Screenable and Easily Searchable Database of Computationally Created Chemical Compounds Optimized toward High Likelihood of Synthetic Tractability. 1824-1835
• 
  Paola Bisignano, Neil T. Burford, Yi Shang, Brennica Marlow, Kathryn E. Livingston, Abigail M. Fenton, Kristin Rockwell, Lauren Budenholzer, John R. Traynor, Samuel W. Gerritz, Andrew Alt, Marta Filizola:
  Ligand-Based Discovery of a New Scaffold for Allosteric Modulation of the μ-Opioid Receptor. 1836-1843
• 
  Marco Foscato, Benjamin J. Houghton, Giovanni Occhipinti, Robert J. Deeth, Vidar R. Jensen:
  Ring Closure To Form Metal Chelates in 3D Fragment-Based de Novo Design. 1844-1856

Computational Chemistry

• 
  Andrea Bortolato, Francesca Deflorian, Dahlia R. Weiss, Jonathan S. Mason:
  Decoding the Role of Water Dynamics in Ligand-Protein Unbinding: CRF₁R as a Test Case. 1857-1866

Computational Biochemistry

• 
  Williams E. Miranda, Sergei Yu Noskov, Pedro A. Valiente:
  Improving the LIE Method for Binding Free Energy Calculations of Protein-Ligand Complexes. 1867-1877
• 
  Francesco Raimondi, Angelo Felline, Francesca Fanelli:
  Catching Functional Modes and Structural Communication in Dbl Family Rho Guanine Nucleotide Exchange Factors. 1878-1893
• 
  Wasinee Khuntawee, Peter Wolschann, Thanyada Rungrotmongkol, Jirasak Wong-ekkabut, Supot Hannongbua:
  Molecular Dynamics Simulations of the Interaction of Beta Cyclodextrin with a Lipid Bilayer. 1894-1902
• 
  Jianzhong Chen, Xingyu Wang, Tong Zhu, Qinggang Zhang, John Z. H. Zhang:
  A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods. 1903-1913
• 
  In-Hee Park, John D. Venable, Caitlin Steckler, Susan E. Cellitti, Scott A. Lesley, Glen Spraggon, Ansgar Brock:
  Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis. 1914-1925
• 
  Ming Kuang, Jingwei Zhou, Laiyou Wang, Zhihong Liu, Jiao Guo, Ruibo Wu:
  Binding Kinetics versus Affinities in BRD4 Inhibition. 1926-1935
• 
  Hung Nguyen, Tien Tran, Yoshifumi Fukunishi, Junichi Higo, Haruki Nakamura, Ly Le:
  Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method. 1936-1943

Pharmaceutical Modeling

• 
  Jennifer Degac, Uwe Winter, Volkhard Helms:
  Graph-Based Clustering of Predicted Ligand-Binding Pockets on Protein Surfaces. 1944-1952
• 
  Jacob D. Durrant, Kathryn E. Carlson, Teresa A. Martin, Tavina L. Offutt, Christopher G. Mayne, John A. Katzenellenbogen, Rommie E. Amaro:
  Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands. 1953-1961
• 
  Ionut Onila, Tim ten Brink, Kai Fredriksson, Luca Codutti, Adam Mazur, Christian Griesinger, Teresa Carlomagno, Thomas E. Exner:
  On-the-Fly Integration of Data from a Spin-Diffusion-Based NMR Experiment into Protein-Ligand Docking. 1962-1972
• 
  Xuben Hou, Kangshuai Li, Xiao Yu, Jin-peng Sun, Hao Fang:
  Protein Flexibility in Docking-Based Virtual Screening: Discovery of Novel Lymphoid-Specific Tyrosine Phosphatase Inhibitors Using Multiple Crystal Structures. 1973-1983
• 
  Fredrik Svensson, Karin Engen, Thomas Lundbäck, Mats Larhed, Christian Sköld:
  Virtual Screening for Transition State Analogue Inhibitors of IRAP Based on Quantum Mechanically Derived Reaction Coordinates. 1984-1993
• 
  Yu Zhang, Lei Xu, Zhiqiang Zhang, Zhiyu Zhang, Longtai Zheng, Dan Li, Youyong Li, Feng Liu, Kunqian Yu, Tingjun Hou, Xuechu Zhen:
  Structure-Activity Relationships and Anti-inflammatory Activities of N-Carbamothioylformamide Analogues as MIF Tautomerase Inhibitors. 1994-2004

Bioinformatics

• 
  Franck Da Silva, Jérémy Desaphy, Guillaume Bret, Didier Rognan:
  IChemPIC: A Random Forest Classifier of Biological and Crystallographic Protein-Protein Interfaces. 2005-2014
• 
  Shuyan Li, Jiazhong Li, Lulu Ning, Shaopeng Wang, Yuzhen Niu, Nengzhi Jin, Xiaojun Yao, Huanxiang Liu, Lili Xi:
  In Silico Identification of Protein S-Palmitoylation Sites and Their Involvement in Human Inherited Disease. 2015-2025
• 
  Andrzej Galat:
  Multidimensional Drift of Sequence Attributes and Functional Profiles in the Superfamily of the Three-Finger Proteins and Their Structural Homologues. 2026-2041
• 
  Fei Guo, Yijie Ding, Zhao Li, Jijun Tang:
  Identification of Protein-Protein Interactions by Detecting Correlated Mutation at the Interface. 2042-2049
• 
  Bartlomiej Zaborowski, Dawid Jagiela, Cezary Czaplewski, Anna Halabis, Agnieszka Lewandowska, Wioletta Zmudzinska, Stanislaw Oldziej, Agnieszka S. Karczynska, Christian Omieczynski, Tomasz K. Wirecki, Adam Liwo:
  A Maximum-Likelihood Approach to Force-Field Calibration. 2050-2070

Volume 55, Number 10, October 2015

Application Notes

• 
  Matthias Hilbig, Matthias Rarey:
  MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing. 2071-2078

Letters

• 
  Weijun Xu, Junxian Lim, Chai-Yeen Goh, Jacky Y. Suen, Yuhong Jiang, Mei-Kwan Yau, Kai-Chen Wu, Ligong Liu, David P. Fairlie:
  Repurposing Registered Drugs as Antagonists for Protease-Activated Receptor 2. 2079-2084

Chemical Information

• 
  Youjun Xu, Ziwei Dai, Fangjin Chen, Shuaishi Gao, Jianfeng Pei, Luhua Lai:
  Deep Learning for Drug-Induced Liver Injury. 2085-2093
• 
  Daimel Castillo-González, Jean-Louis Mergny, Aurore De Rache, Gisselle Pérez-Machado, Miguel Ángel Cabrera-Pérez, Orazio Nicolotti, Antonellina Introcaso, Giuseppe Felice Mangiatordi, Aurore Guédin, Anne Bourdoncle, Teresa M. Garrigues, Federico Pallardó, M. Natália Dias Soeiro Cordeiro, Cesar Paz-y-Miño, Eduardo Tejera, Fernanda Borges, Maykel Cruz-Monteagudo:
  Harmonization of QSAR Best Practices and Molecular Docking Provides an Efficient Virtual Screening Tool for Discovering New G-Quadruplex Ligands. 2094-2110
• 
  Nadine Schneider, Roger A. Sayle, Gregory A. Landrum:
  Get Your Atoms in Order - An Open-Source Implementation of a Novel and Robust Molecular Canonicalization Algorithm. 2111-2120

Computational Chemistry

• 
  A. Y. Lizunov, A. L. Gonchar, Natalia Zaitseva, Viktor Zosimov:
  Accounting for Intraligand Interactions in Flexible Ligand Docking with a PMF-Based Scoring Function. 2121-2137
• 
  Xuejin Zhang, Zhen Gong, Jian Li, Tao Lu:
  Intermolecular Sulfur···Oxygen Interactions: Theoretical and Statistical Investigations. 2138-2153
• 
  Hannah H. Avgy-David, Hanoch Senderowitz:
  Toward Focusing Conformational Ensembles on Bioactive Conformations: A Molecular Mechanics/Quantum Mechanics Study. 2154-2167
• 
  Agata Kurczyk, Dawid Warszycki, Robert Musiol, Rafal Kafel, Andrzej J. Bojarski, Jaroslaw Polanski:
  Ligand-Based Virtual Screening in a Search for Novel Anti-HIV-1 Chemotypes. 2168-2177
• 
  I-Chung Cheng, Ya-Jyun Chen, Chia-Wei Ku, Yu-Wen Huang, Chia-Ning Yang:
  Structural and Dynamic Characterization of Mutated Keap1 for Varied Affinity toward Nrf2: A Molecular Dynamics Simulation Study. 2178-2186
• 
  Wesley M. Botello-Smith, Ray Luo:
  Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation. 2187-2199
• 
  Noelia Ferruz, Matthew J. Harvey, Jordi Mestres, Gianni De Fabritiis:
  Insights from Fragment Hit Binding Assays by Molecular Simulations. 2200-2205

Computational Biochemistry

• 
  Catarina A. Carvalheda, Sara R. R. Campos, António M. Baptista:
  The Effect of Membrane Environment on Surfactant Protein C Stability Studied by Constant-pH Molecular Dynamics. 2206-2217
• 
  Jacopo Sgrignani, Marcella Iannuzzi, Alessandra Magistrato:
  Role of Water in the Puzzling Mechanism of the Final Aromatization Step Promoted by the Human Aromatase Enzyme. Insights from QM/MM MD Simulations. 2218-2226
• 
  Luca Mollica, Gianluca Conti, Loredano Pollegioni, Andrea Cavalli, Elena Rosini:
  Unveiling the Atomic-Level Determinants of Acylase-Ligand Complexes: An Experimental and Computational Study. 2227-2241
• 
  Petr Popov, Sergei Grudinin:
  Knowledge of Native Protein-Protein Interfaces Is Sufficient To Construct Predictive Models for the Selection of Binding Candidates. 2242-2255

Pharmaceutical Modeling

• 
  Francesca Spyrakis, Paolo Benedetti, Sergio Decherchi, Walter Rocchia, Andrea Cavalli, Stefano Alcaro, Francesco Ortuso, Massimo Baroni, Gabriele Cruciani:
  A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins. 2256-2274

Bioinformatics

• 
  Mara Kozic, Damir Vukicevic, Juraj Simunic, Tomislav Roncevic, Nikolinka Antcheva, Alessandro Tossi, Davor Juretic:
  Predicting the Minimal Inhibitory Concentration for Antimicrobial Peptides with Rana-Box Domain. 2275-2287

Software Description

• 
  Mikolaj Feliks, Martin J. Field:
  Pcetk: A pDynamo-based Toolkit for Protonation State Calculations in Proteins. 2288-2296

Volume 55, Number 11, November 2015

Application Notes

• 
  Tamer M. Ibrahim, Matthias R. Bauer, Alexander Dörr, Erdem Veyisoglu, Frank M. Boeckler:
  pROC-Chemotype Plots Enhance the Interpretability of Benchmarking Results in Structure-Based Virtual Screening. 2297-2307
• 
  Janez Konc, Benjamin T. Miller, Tanja Stular, Samo Lesnik, H. Lee Woodcock III, Bernard R. Brooks, Dusanka Janezic:
  ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. 2308-2314

Chemical Information

• 
  Julian E. Fuchs, Bernd Wellenzohn, Nils Weskamp, Klaus R. Liedl:
  Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications. 2315-2323
• 
  Teague Sterling, John J. Irwin:
  ZINC 15 - Ligand Discovery for Everyone. 2324-2337

Computational Chemistry

• 
  Adriana Supady, Volker Blum, Carsten Baldauf:
  First-Principles Molecular Structure Search with a Genetic Algorithm. 2338-2348
• 
  Michael Zhenin, Efrat Noy, Hanoch Senderowitz:
  REMD Simulations Reveal the Dynamic Profile and Mechanism of Action of Deleterious, Rescuing, and Stabilizing Perturbations to NBD1 from CFTR. 2349-2364
• 
  Roberto Todeschini, Davide Ballabio, Matteo Cassotti, Viviana Consonni:
  N3 and BNN: Two New Similarity Based Classification Methods in Comparison with Other Classifiers. 2365-2374
• 
  Rosa Buonfiglio, Ola Engkvist, Péter L. Várkonyi, Astrid Henz, Elisabet Vikeved, Anders Backlund, Thierry Kogej:
  Investigating Pharmacological Similarity by Charting Chemical Space. 2375-2390
• 
  Rosa L. Camacho-Mendoza, Evelin Gutiérrez-Moreno, Edmundo Guzmán-Percástegui, Eliazar Aquino-Torres, Julián Cruz-Borbolla, José A. Rodríguez-Ávila, José G. Alvarado-Rodríguez, Oscar Olvera-Neria, Pandiyan Thangarasu, José L. Medina-Franco:
  Density Functional Theory and Electrochemical Studies: Structure-Efficiency Relationship on Corrosion Inhibition. 2391-2402
• 
  Héléna A. Gaspar, Igor I. Baskin, Gilles Marcou, Dragos Horvath, Alexandre Varnek:
  Stargate GTM: Bridging Descriptor and Activity Spaces. 2403-2410
• 
  Thomas B. Steinbrecher, Markus K. Dahlgren, Daniel Cappel, Teng Lin, Lingle Wang, Goran Krilov, Robert Abel, Richard A. Friesner, Woody Sherman:
  Accurate Binding Free Energy Predictions in Fragment Optimization. 2411-2420

Pharmaceutical Modeling

• 
  Damian Bartuzi, Agnieszka A. Kaczor, Dariusz Matosiuk:
  Activation and Allosteric Modulation of Human μ Opioid Receptor in Molecular Dynamics. 2421-2434
• 
  Ran Cao, Yanli Wang, Niu Huang:
  Discovery of 2-Acylaminothiophene-3-Carboxamides as Multitarget Inhibitors for BCR-ABL Kinase and Microtubules. 2435-2442
• 
  Roberta Fazi, Cristina Tintori, Annalaura Brai, Lorenzo Botta, Manikandan Selvaraj, Anna Garbelli, Giovanni Maga, Maurizio Botta:
  Homology Model-Based Virtual Screening for the Identification of Human Helicase DDX3 Inhibitors. 2443-2454
• 
  Lu Cui, Yu Wang, Zhihong Liu, Hongzhuan Chen, Hao Wang, Xinxin Zhou, Jun Xu:
  Discovering New Acetylcholinesterase Inhibitors by Mining the Buzhongyiqi Decoction Recipe Data. 2455-2463

Bioinformatics

• 
  Feng Xiao, Hong-Bin Shen:
  Prediction Enhancement of Residue Real-Value Relative Accessible Surface Area in Transmembrane Helical Proteins by Solving the Output Preference Problem of Machine Learning-Based Predictors. 2464-2474

Software Description

• 
  Magnus Norrby, Christoph Grebner, Joakim Eriksson, Jonas Boström:
  Molecular Rift: Virtual Reality for Drug Designers. 2475-2484

Volume 55, Number 12, December 2015

Application Notes

• 
  Hannes H. Loeffler, Julien Michel, Christopher J. Woods:
  FESetup: Automating Setup for Alchemical Free Energy Simulations. 2485-2490
• 
  Christophe Bovigny, Giorgio Tamò, Thomas Lemmin, Nicolas Maïno, Matteo Dal Peraro:
  LipidBuilder: A Framework To Build Realistic Models for Biological Membranes. 2491-2499

Chemical Information

• 
  Michael Fernández, Hongqing Shi, Amanda S. Barnard:
  Quantitative Structure-Property Relationship Modeling of Electronic Properties of Graphene Using Atomic Radial Distribution Function Scores. 2500-2506
• 
  Oren E. Nahum, Abraham Yosipof, Hanoch Senderowitz:
  A Multi-Objective Genetic Algorithm for Outlier Removal. 2507-2518

Computational Chemistry

• 
  Zheng Shao, Yuya Hirayama, Yoshihiro Yamanishi, Hiroto Saigo:
  Mining Discriminative Patterns from Graph Data with Multiple Labels and Its Application to Quantitative Structure-Activity Relationship (QSAR) Models. 2519-2527
• 
  Giovanni Grazioso, Jacopo Sgrignani, Romina Capelli, Carlo Matera, Clelia Dallanoce, Marco De Amici, Andrea Cavalli:
  Allosteric Modulation of Alpha7 Nicotinic Receptors: Mechanistic Insight through Metadynamics and Essential Dynamics. 2528-2539
• 
  Rosella Ombrato, Nicola Cazzolla, Francesca Mancini, Giorgina Mangano:
  Structure-Based Discovery of 1H-Indazole-3-carboxamides as a Novel Structural Class of Human GSK-3 Inhibitors. 2540-2551
• 
  Yenny Villuendas-Rey, Juan Raúl Alvarez-Idaboy, Annia Galano:
  Assessing the Protective Activity of a Recently Discovered Phenolic Compound against Oxidative Stress Using Computational Chemistry. 2552-2561
• 
  Sereina Riniker, Gregory A. Landrum:
  Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation. 2562-2574

Computational Biochemistry

• 
  Yang Jiang, Haiyang Zhang, Wei Feng, Tianwei Tan:
  Refined Dummy Atom Model of Mg²⁺ by Simple Parameter Screening Strategy with Revised Experimental Solvation Free Energy. 2575-2586
• 
  Micholas Dean Smith, J. Srinivasa Rao, Elizabeth Segelken, Luis Cruz:
  Force-Field Induced Bias in the Structure of Aβ_21-30: A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields. 2587-2595
• 
  Faezeh Shirgahi Talari, Kowsar Bagherzadeh, Sahand Golestanian, Michael Jarstfer, Massoud Amanlou:
  Potent Human Telomerase Inhibitors: Molecular Dynamic Simulations, Multiple Pharmacophore-Based Virtual Screening, and Biochemical Assays. 2596-2610
• 
  Ylenia Cau, Annarita Fiorillo, Mattia Mori, Andrea Ilari, Maurizio Botta, Marco Lalle:
  Molecular Dynamics Simulations and Structural Analysis of Giardia duodenalis 14-3-3 Protein-Protein Interactions. 2611-2622
• 
  Ran Zhou, Yiqian Xie, Hao Hu, Guang Hu, Viral Sanjay Patel, Jin Zhang, Kunqian Yu, Yiran Huang, Hualiang Jiang, Zhongjie Liang, Yujun George Zheng, Cheng Luo:
  Molecular Mechanism underlying PRMT1 Dimerization for SAM Binding and Methylase Activity. 2623-2632
• 
  Maria Pechlaner, Chris Oostenbrink:
  Multiple Binding Poses in the Hydrophobic Cavity of Bee Odorant Binding Protein AmelOBP14. 2633-2643
• 
  P. Haris, Mary Varughese, M. Haridas, C. Sudarsanakumar:
  Energetics, Thermodynamics, and Molecular Recognition of Piperine with DNA. 2644-2656
• 
  Joshua Pottel, Nicolas Moitessier:
  Single-Point Mutation with a Rotamer Library Toolkit: Toward Protein Engineering. 2657-2671
• 
  Melek N. Ucisik, Sharon Hammes-Schiffer:
  Comparative Molecular Dynamics Studies of Human DNA Polymerase η. 2672-2681

Pharmaceutical Modeling

• 
  Isidro Cortes-Ciriano, Andreas Bender:
  Improved Chemical Structure-Activity Modeling Through Data Augmentation. 2682-2692
• 
  Peichen Pan, Sheng Tian, Huiyong Sun, Xiaotian Kong, Wenfang Zhou, Dan Li, Youyong Li, Tingjun Hou:
  Identification and Preliminary SAR Analysis of Novel Type-I Inhibitors of TIE-2 via Structure-Based Virtual Screening and Biological Evaluation in in vitro Models. 2693-2704

Bioinformatics

• 
  Hiroaki Iwata, Ryusuke Sawada, Sayaka Mizutani, Masaaki Kotera, Yoshihiro Yamanishi:
  Large-Scale Prediction of Beneficial Drug Combinations Using Drug Efficacy and Target Profiles. 2705-2716
• 
  Ryusuke Sawada, Hiroaki Iwata, Sayaka Mizutani, Yoshihiro Yamanishi:
  Target-Based Drug Repositioning Using Large-Scale Chemical-Protein Interactome Data. 2717-2730
• 
  Quan Van Vuong, Tin Trung Nguyen, Mai Suan Li:
  A New Method for Navigating Optimal Direction for Pulling Ligand from Binding Pocket: Application to Ranking Binding Affinity by Steered Molecular Dynamics. 2731-2738