Journal of Chemical Information and Modeling, Volume 52

Volume 52, Number 1, January 2012

Letters

• 
  Edgar A. Gatica, Claudio N. Cavasotto:
  Ligand and Decoy Sets for Docking to G Protein-Coupled Receptors. 1-6

Chemical Information

• 
  Kuei-Jen Lee:
  Molecular Dynamics Simulations of a Hyperthermophilic and a Mesophilic Protein L30e. 7-15
• 
  Jui-Hua Hsieh, Shuangye Yin, Xiang S. Wang, Shubin Liu, Nikolay V. Dokholyan, Alexander Tropsha:
  Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening. 16-28
• 
  S. Joshua Swamidass, Bradley T. Calhoun, Joshua A. Bittker, Nicole E. Bodycombe, Paul A. Clemons:
  Utility-Aware Screening with Clique-Oriented Prioritization. 29-37
• 
  Xia Ning, Michael A. Walters, George Karypis:
  Improved Machine Learning Models for Predicting Selective Compounds. 38-50
• 
  Roger A. Sayle, Paul Hongxing Xie, Sorel Muresan:
  Improved Chemical Text Mining of Patents with Infinite Dictionaries and Automatic Spelling Correction. 51-62

Computational Chemistry

• 
  Jing Shi, Xiong-Yi Huang, Hua-Jing Wang, Yao Fu:
  Hydride Dissociation Energies of Six-Membered Heterocyclic Organic Hydrides Predicted by ONIOM-G4Method. 63-75
• 
  Wasinee Khuntawee, Thanyada Rungrotmongkol, Supot Hannongbua:
  Molecular Dynamic Behavior and Binding Affinity of Flavonoid Analogues to the Cyclin Dependent Kinase 6/cyclin D Complex. 76-83
• 
  Eric L. First, Chrysanthos E. Gounaris, Christodoulos A. Floudas:
  Stereochemically Consistent Reaction Mapping and Identification of Multiple Reaction Mechanisms through Integer Linear Optimization. 84-92
• 
  Sadhana Kumbhar, Frank D. Fischer, Mark P. Waller:
  Assessment of Weak Intermolecular Interactions Across QM/MM Noncovalent Boundaries. 93-98
• 
  Sebastian A. Andujar, Rodrigo D. Tosso, Fernando D. Suvire, Emilio Angelina, Nelida Peruchena, Nuria Cabedo, Diego Cortes, Ricardo D. Enriz:
  Searching the "Biologically Relevant"Conformation of Dopamine: A Computational Approach. 99-112

Computational Biochemistry

• 
  M. Victoria Ruiz-Pérez, Almudena Pino-Ángeles, Miguel Angel Medina, Francisca Sánchez-Jiménez, Aurelio A. Moya-García:
  Structural Perspective on the Direct Inhibition Mechanism of EGCG on Mammalian Histidine Decarboxylase and DOPA Decarboxylase. 113-119
• 
  Alexander Metz, Christopher Pfleger, Hannes Kopitz, Stefania Pfeiffer-Marek, Karl-Heinz Baringhaus, Holger Gohlke:
  Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein-Protein Interface. 120-133

Pharmaceutical Modeling

• 
  Zoltán Simon, Ágnes Peragovics, Margit Vigh-Smeller, Gábor Csukly, László Tombor, Zhenhui Yang, Gergely Zahoránszky-Köhalmi, László Végner, Balázs Jelinek, Péter Hári, Csaba Hetényi, István Bitter, Pál Czobor, András Málnási-Csizmadia:
  Drug Effect Prediction by Polypharmacology-Based Interaction Profiling. 134-145
• 
  Kuei-Chung Shih, Chun-Yuan Lin, Hsiao-Chieh Chi, Chrong-Shiong Hwang, Ting-Shou Chen, Chuan Yi Tang, Naiwan Hsiao:
  Design of Novel FLT-3 Inhibitors Based on Dual-Layer 3D-QSAR Model and Fragment-Based Compounds in Silico. 146-155
• 
  Eric J. Martin, Prasenjit Mukherjee:
  Kinase-Kernel Models: Accurate In silico Screening of 4 Million Compounds Across the Entire Human Kinome. 156-170
• 
  Zhaomin Liu, A. Michael Crider, Daniel Ansbro, Christina Hayes, Maria Kontoyianni:
  A Structure-Based Approach to Understanding Somatostatin Receptor-4 Agonism (sst4). 171-186
• 
  Mengang Xu, Markus A. Lill:
  Utilizing Experimental Data for Reducing Ensemble Size in Flexible-Protein Docking. 187-198
• 
  David R. Hall, Chi-Ho Ngan, Brandon S. Zerbe, Dima Kozakov, Sandor Vajda:
  Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery. 199-209
• 
  Eric Therrien, Pablo Englebienne, Andrew G. Arrowsmith, Rodrigo Mendoza-Sanchez, Christopher R. Corbeil, Nathanael Weill, Valérie Campagna-Slater, Nicolas Moitessier:
  Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with Forecaster, a Novel Platform for Drug Discovery. 210-224
• 
  Fredrik Svensson, Anders Karlén, Christian Sköld:
  Virtual Screening Data Fusion Using Both Structure- and Ligand-Based Methods. 225-232
• 
  Robert Kiss, Mark Sandor, Anikó Gere, Éva Schmidt, György Balogh, Béla Kiss, László Molnár, Christian Lemmen, György M. Keserü:
  Discovery of Novel Histamine H4 and Serotonin Transporter Ligands Using the Topological Feature Tree Descriptor. 233-242
• 
  Varnavas D. Mouchlis, Vasiliki Michopoulou, Violetta Constantinou-Kokotou, Thomas M. Mavromoustakos, Edward A. Dennis, George Kokotos:
  Binding Conformation of 2-Oxoamide Inhibitors to Group IVA Cytosolic Phospholipase A₂ Determined by Molecular Docking Combined with Molecular Dynamics. 243-254

Software Description

• 
  Márton Münz, Philip C. Biggin:
  JGromacs: A Java Package for Analyzing Protein Simulations. 255-259
• 
  Vladimir V. Diky, Robert D. Chirico, Chris Muzny, Andrei F. Kazakov, Kenneth Kroenlein, Joseph W. Magee, Ilmutdin Abdulagatov, Jeong Won Kang, Michael Frenkel:
  ThermoData Engine (TDE) Software Implementation of the Dynamic Data Evaluation Concept. 7. Ternary Mixtures. 260-276

Volume 52, Number 2, February 2012

2011 Noordwijkerhout Cheminformatics
Editorial

• 
  Wendy A. Warr:
  Ninth International Conference on Chemical Structures, June 5-9, 2011, Noordwijkerhout, The Netherlands. 277

Chemical Information

• 
  Man-Ling Lee, Ignacio Aliagas, Jennafer Dotson, Jianwen A. Feng, Alberto Gobbi, Timothy Heffron:
  DEGAS: Sharing and Tracking Target Compound Ideas with External Collaborators. 278-284
• 
  Alberto Gobbi, Man-Ling Lee:
  Handling of Tautomerism and Stereochemistry in Compound Registration. 285-292
• 
  Felix Rudolphi, Lukas J. Goossen:
  Electronic Laboratory Notebook: The Academic Point of View. 293-301
• 
  Paolo Tosco, Thomas Balle:
  A 3D-QSAR-Driven Approach to Binding Mode and Affinity Prediction. 302-307
• 
  Richard L. Martin, Berend Smit, Maciej Haranczyk:
  Addressing Challenges of Identifying Geometrically Diverse Sets of Crystalline Porous Materials. 308-318
• 
  Pekka Tiikkainen, Lutz Franke:
  Analysis of Commercial and Public Bioactivity Databases. 319-326
• 
  Lionel Colliandre, Vincent Le Guilloux, Stéphane Bourg, Luc Morin-Allory:
  Visual Characterization and Diversity Quantification of Chemical Libraries: 2. Analysis and Selection of Size-Independent, Subspace-Specific Diversity Indices. 327-342
• 
  David Sehnal, Radka Svobodová Vareková, Heinrich J. Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová, Jaroslav Koca:
  SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. 343-359
• 
  Andrea Volkamer, Daniel Kuhn, Thomas Grombacher, Friedrich Rippmann, Matthias Rarey:
  Combining Global and Local Measures for Structure-Based Druggability Predictions. 360-372
• 
  Uta F. Lessel, Bernd Wellenzohn, J. Robert Fischer, Matthias Rarey:
  Design of Combinatorial Libraries for the Exploration of Virtual Hits from Fragment Space Searches with LoFT. 373-379

Computational Chemistry

• 
  Modest von Korff, Joël Freyss, Thomas Sander, Christoph Boss, Claire-Lise Ciana:
  Fighting High Molecular Weight in Bioactive Molecules with Sub-Pharmacophore-Based Virtual Screening. 380-390

Letters

• 
  Jennifer A. Bayron, Amy M. Deveau, John M. Stubbs:
  Conformational Analysis of 6α- and 6β-Naltrexol and Derivatives and Relationship to Opioid Receptor Affinity. 391-395

Chemical Information

• 
  Kunal Roy, Indrani Mitra, Supratik Kar, Probir Kumar Ojha, Rudra Narayan Das, Humayun Kabir:
  Comparative Studies on Some Metrics for External Validation of QSPR Models. 396-408

Computational Chemistry

• 
  Jacob Poehlsgaard, Kasper Harpsøe, Flemming Steen Jørgensen, Lars Olsen:
  A Robust Force Field Based Method for Calculating Conformational Energies of Charged Drug-Like Molecules. 409-419
• 
  Jogoth Ali, Patrick Camilleri, Marc B. Brown, Andrew J. Hutt, Stewart B. Kirton:
  Revisiting the General Solubility Equation: In Silico Prediction of Aqueous Solubility Incorporating the Effect of Topographical Polar Surface Area. 420-428
• 
  Jana Sopkova-de Oliveira Santos, Anne Sophie Voisin-Chiret, Gregory Burzicki, Laure Sebaoun, Muriel Sebban, Jean-François Lohier, Rémi Legay, Hassan Oulyadi, Ronan Bureau, Sylvain Rault:
  Structural Characterizations of Oligopyridyl Foldamers, α-Helix Mimetics. 429-439
• 
  Se-Han Lee, Kwang-Hwi Cho, William E. Acree Jr., Kyoung Tai No:
  Development of Surface-SFED Models for Polar Solvents. 440-448

Computational Biochemistry

• 
  Jianzhuang Yao, Yuzhuo Chu, Ran An, Hong Guo:
  Understanding Product Specificity of Protein Lysine Methyltransferases from QM/MM Molecular Dynamics and Free Energy Simulations: The Effects of Mutation on SET7/9 beyond the Tyr/Phe Switch. 449-456
• 
  Johanna Jyrkkärinne, Jenni Küblbeck, Juha Pulkkinen, Paavo Honkakoski, Reino Laatikainen, Antti Poso, Tuomo Laitinen:
  Molecular Dynamics Simulations for Human CAR Inverse Agonists. 457-464
• 
  Diana Lousa, António M. Baptista, Cláudio M. Soares:
  Analyzing the Molecular Basis of Enzyme Stability in Ethanol/Water Mixtures Using Molecular Dynamics Simulations. 465-473
• 
  Luisa Di Paola, Paola Paci, Daniele Santoni, Micol De Ruvo, Alessandro Giuliani:
  Proteins as Sponges: A Statistical Journey along Protein Structure Organization Principles. 474-482
• 
  Matteo Chioccioli, Simone Marsili, Claudia Bonaccini, Piero Procacci, Paola Gratteri:
  Insights into the Conformational Switching Mechanism of the Human Vascular Endothelial Growth Factor Receptor Type 2 Kinase Domain. 483-491

Pharmaceutical Modeling

• 
  Mohamed Diwan M. AbdulHameed, Sidhartha Chaudhury, Narender Singh, Hongmao Sun, Anders Wallqvist, Gregory J. Tawa:
  Exploring Polypharmacology Using a ROCS-Based Target Fishing Approach. 492-505
• 
  Ying-Ting Lin, Guan-Yu Chen:
  A Scaffold-Independent Subcellular Event-Based Analysis: Characterization of Significant Structural Modifications. 506-514
• 
  Horrick Sharma, Xiaolin Cheng, John K. Buolamwini:
  Homology Model-Guided 3D-QSAR Studies of HIV-1 Integrase Inhibitors. 515-544

Bioinformatics

• 
  Francesco Bettella, Dawid Rasinski, Ernst-Walter Knapp:
  Protein Secondary Structure Prediction with SPARROW. 545-556
• 
  Satoshi Yamasaki, Shugo Nakamura, Kazuhiko Fukui:
  Prospects for Tertiary Structure Prediction of RNA Based on Secondary Structure Information. 557-567
• 
  Valère Lounnas, Gert Vriend:
  AsteriX: A Web Server To Automatically Extract Ligand Coordinates from Figures in PDF Articles. 568-576
• 
  Michael Binns, Sam P. de Visser, Constantinos Theodoropoulos:
  Modeling Flexible Pharmacophores with Distance Geometry, Scoring, and Bound Stretching. 577-588
• 
  Subha Kalyaanamoorthy, Yi-Ping Phoebe Chen:
  Exploring Inhibitor Release Pathways in Histone Deacetylases Using Random Acceleration Molecular Dynamics Simulations. 589-603
• 
  Janez Konc, Tomo Cesnik, Joanna Trykowska Konc, Matej Penca, Dusanka Janezic:
  ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of PDB Structures. 604-612

Computer Software Reviews

• 
  Matthew C. Swain:
  chemicalize.org. 613-615

Volume 52, Number 3, March 2012

Perspectives

• 
  Johannes Kirchmair, Mark J. Williamson, Jonathan D. Tyzack, Lu Tan, Peter J. Bond, Andreas Bender, Robert C. Glen:
  Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms. 617-648

Letters

• 
  Stefano Alcaro, Adriana Bolasco, Roberto Cirilli, Rosella Ferretti, Rossella Fioravanti, Francesco Ortuso:
  Computer-Aided Molecular Design of Asymmetric Pyrazole Derivatives with Exceptional Enantioselective Recognition toward the Chiralcel OJ-H Stationary Phase. 649-654

Chemical Information

• 
  Feixiong Cheng, Yutaka Ikenaga, Yadi Zhou, Yue Yu, Weihua Li, Jie Shen, Zheng Du, Lei Chen, Congying Xu, Guixia Liu, Philip W. Lee, Yun Tang:
  In Silico Assessment of Chemical Biodegradability. 655-669
• 
  Ye Hu, Jürgen Bajorath:
  Exploration of 3D Activity Cliffs on the Basis of Compound Binding Modes and Comparison of 2D and 3D Cliffs. 670-677

Computational Chemistry

• 
  Tammy Biniashvili, Ehud Schreiber, Yossef Kliger:
  Improving Classical Substructure-Based Virtual Screening to Handle Extrapolation Challenges. 678-685
• 
  Ya-Wen Hsiao, Carl Petersson, Mats Svensson, Ulf Norinder:
  A Pragmatic Approach Using First-Principle Methods to Address Site of Metabolism with Implications for Reactive Metabolite Formation. 686-695
• 
  Falgun Shah, Jiri Gut, Jennifer Legac, Devleena Shivakumar, Woody Sherman, Philip J. Rosenthal, Mitchell A. Avery:
  Computer-Aided Drug Design of Falcipain Inhibitors: Virtual Screening, Structure-Activity Relationships, Hydration Site Thermodynamics, and Reactivity Analysis. 696-710
• 
  Varnavas D. Mouchlis, Georgia Melagraki, Thomas M. Mavromoustakos, George Kollias, Antreas Afantitis:
  Molecular Modeling on Pyrimidine-Urea Inhibitors of TNF-α Production: An Integrated Approach Using a Combination of Molecular Docking, Classification Techniques, and 3D-QSAR CoMSIA. 711-723
• 
  Miklos Feher, Christopher I. Williams:
  Numerical Errors and Chaotic Behavior in Docking Simulations. 724-738

Computational Biochemistry

• 
  Markus Sitzmann, Iwona E. Weidlich, Igor V. Filippov, Chenzhong Liao, Megan L. Peach, Wolf-Dietrich Ihlenfeldt, Rajeshri G. Karki, Yulia V. Borodina, Raul E. Cachau, Marc C. Nicklaus:
  PDB Ligand Conformational Energies Calculated Quantum-Mechanically. 739-756

Pharmaceutical Modeling

• 
  Richard L. Martin, Eleanor J. Gardiner, Stefan Senger, Valerie J. Gillet:
  Compression of Molecular Interaction Fields Using Wavelet Thumbnails: Application to Molecular Alignment. 757-769
• 
  Karim M. ElSawy, Reidun Twarock, Chandra S. Verma, Leo S. D. Caves:
  Peptide Inhibitors of Viral Assembly: A Novel Route to Broad-Spectrum Antivirals. 770-776
• 
  Prashant Khare, Amit K. Gupta, Praveen K. Gajula, Krishna Y. Sunkari, Anil K. Jaiswal, Sanchita Das, Preeti Bajpai, Tushar K. Chakraborty, Anuradha Dube, Anil K. Saxena:
  Identification of Novel S-Adenosyl-l-Homocysteine Hydrolase Inhibitors through Homology-Model-Based Virtual Screening, Synthesis, and Biological Evaluation. 777-791
• 
  Bin Chen, Robert P. Sheridan, Viktor Hornak, Johannes H. Voigt:
  Comparison of Random Forest and Pipeline Pilot Naïve Bayes in Prospective QSAR Predictions. 792-803
• 
  Vojtech Spiwok, Katarína Hlat-Glembová, Igor Tvaroska, Blanka Králová:
  Conformational Free Energy Modeling of Druglike Molecules by Metadynamics in the WHIM Space. 804-813
• 
  Robert P. Sheridan:
  Three Useful Dimensions for Domain Applicability in QSAR Models Using Random Forest. 814-823

Bioinformatics

• 
  Maria Kontoyianni, Christopher B. Rosnick:
  Functional Prediction of Binding Pockets. 824-833
• 
  Hong Kang, Zhen Sheng, Ruixin Zhu, Qi Huang, Qi Liu, Zhiwei Cao:
  Virtual Drug Screen Schema Based on Multiview Similarity Integration and Ranking Aggregation. 834-843
• 
  Matthias Dietzen, Elena Zotenko, Andreas Hildebrandt, Thomas Lengauer:
  On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking. 844-856
• 
  Frank H. Allen, Colin R. Groom, John W. Liebeschuetz, David A. Bardwell, Tjelvar S. G. Olsson, Peter A. Wood:
  The Hydrogen Bond Environments of 1H-Tetrazole and Tetrazolate Rings: The Structural Basis for Tetrazole-Carboxylic Acid Bioisosterism. 857-866

Volume 52, Number 4, April 2012

Perspectives

• 
  Thomas Scior, Andreas Bender, Gary Tresadern, José L. Medina-Franco, Karina Martínez-Mayorga, Thierry Langer, Karina Cuanalo-Contreras, Dimitris K. Agrafiotis:
  Recognizing Pitfalls in Virtual Screening: A Critical Review. 867-881

Letters

• 
  Cristiano R. W. Guimarães, Alan M. Mathiowetz, Marina Shalaeva, Gilles Goetz, Spiros Liras:
  Use of 3D Properties to Characterize Beyond Rule-of-5 Property Space for Passive Permeation. 882-890

Chemical Information

• 
  Ramzi Nasr, Rares Vernica, Chen Li, Pierre Baldi:
  Speeding Up Chemical Searches Using the Inverted Index: The Convergence of Chemoinformatics and Text Search Methods. 891-900
• 
  Satoshi Niijima, Akira Shiraishi, Yasushi Okuno:
  Dissecting Kinase Profiling Data to Predict Activity and Understand Cross-Reactivity of Kinase Inhibitors. 901-912
• 
  Jianwei Che, Frederick J. King, Bin Zhou, Yingyao Zhou:
  Chemical and Biological Properties of Frequent Screening Hits. 913-926
• 
  Vigneshwaran Namasivayam, Jürgen Bajorath:
  Searching for Coordinated Activity Cliffs Using Particle Swarm Optimization. 927-934
• 
  Disha Gupta-Ostermann, Mathias Wawer, Anne Mai Wassermann, Jürgen Bajorath:
  Graph Mining for SAR Transfer Series. 935-942
• 
  Jamel Meslamani, Jiabo Li, Jon M. Sutter, Adrian Stevens, Hugues-Olivier Bertrand, Didier Rognan:
  Protein-Ligand-Based Pharmacophores: Generation and Utility Assessment in Computational Ligand Profiling. 943-955

Computational Chemistry

• 
  Simon J. Cottrell, Tjelvar S. G. Olsson, Robin Taylor, Jason C. Cole, John W. Liebeschuetz:
  Validating and Understanding Ring Conformations Using Small Molecule Crystallographic Data. 956-962
• 
  Adel Hamza, Ning-Ning Wei, Chang-Guo Zhan:
  Ligand-Based Virtual Screening Approach Using a New Scoring Function. 963-974
• 
  Stefan Brandmaier, Ullrika Sahlin, Igor V. Tetko, Tomas Öberg:
  PLS-Optimal: A Stepwise D-Optimal Design Based on Latent Variables. 975-983
• 
  Jong Young Joung, Ky-Youb Nam, Kwang-Hwi Cho, Kyoung Tai No:
  Ligand Aligning Method for Molecular Docking: Alignment of Property-Weighted Vectors. 984-995
• 
  Qishi Du, Jing Gao, Yu-Tuo Wei, Li-Qin Du, Shu-Qing Wang, Ri-Bo Huang:
  Structure-Based and Multiple Potential Three-Dimensional Quantitative Structure-Activity Relationship (SB-MP-3D-QSAR) for Inhibitor Design. 996-1004

Computational Biochemistry

• 
  Zhiwei Feng, Tingjun Hou, Youyong Li:
  Studies on the Interactions between β₂ Adrenergic Receptor and Gs Protein by Molecular Dynamics Simulations. 1005-1014

Pharmaceutical Modeling

• 
  Tomohiro Sato, Hitomi Yuki, Daisuke Takaya, Shunta Sasaki, Akiko Tanaka, Teruki Honma:
  Application of Support Vector Machine to Three-Dimensional Shape-Based Virtual Screening Using Comprehensive Three-Dimensional Molecular Shape Overlay with Known Inhibitors. 1015-1026
• 
  Emanuele Perola, Lee Herman, Jonathan Weiss:
  Development of a Rule-Based Method for the Assessment of Protein Druggability. 1027-1038
• 
  György G. Ferenczy, György M. Keserü:
  Thermodynamics of Fragment Binding. 1039-1045
• 
  Bingjie Hu, Markus A. Lill:
  Protein Pharmacophore Selection Using Hydration-Site Analysis. 1046-1060
• 
  Ahmed M. El Kerdawy, Christian R. Wick, Matthias Hennemann, Timothy Clark:
  Predicting the Sites and Energies of Noncovalent Intermolecular Interactions Using Local Properties. 1061-1071

Software Description

• 
  Jonas Feldt, Ricardo A. Mata, Johannes M. Dieterich:
  Atomdroid: A Computational Chemistry Tool for Mobile Platforms. 1072-1078

Volume 52, Number 5, May 2012

Letters

• 
  Puneet Kacker, Matteo Masetti, Martina Mangold, Giovanni Bottegoni, Andrea Cavalli:
  Combining Dyad Protonation and Active Site Plasticity in BACE-1 Structure-Based Drug Design. 1079-1085

Chemical Information

• 
  Obdulia Rabal, Julen Oyarzabal:
  Using Novel Descriptor Accounting for Ligand-Receptor Interactions To Define and Visually Explore Biologically Relevant Chemical Space. 1086-1102
• 
  Guoping Hu, Guanglin Kuang, Wen Xiao, Weihua Li, Guixia Liu, Yun Tang:
  Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening. 1103-1113
• 
  Meihua Tu, Brajesh K. Rai, Alan M. Mathiowetz, Mary Didiuk, Jeffrey A. Pfefferkorn, Angel Guzman-Perez, John Benbow, Cristiano R. W. Guimarães, Scot Mente, Matthew M. Hayward, Spiros Liras:
  Exploring Aromatic Chemical Space with NEAT: Novel and Electronically Equivalent Aromatic Template. 1114-1123
• 
  Edward O. Cannon:
  New Benchmark for Chemical Nomenclature Software. 1124-1131
• 
  Dongyue Cao, Junmei Wang, Rui Zhou, Youyong Li, Huidong Yu, Tingjun Hou:
  ADMET Evaluation in Drug Discovery. 11. PharmacoKinetics Knowledge Base (PKKB): A Comprehensive Database of Pharmacokinetic and Toxic Properties for Drugs. 1132-1137
• 
  Xiaoying Hu, Ye Hu, Martin Vogt, Dagmar Stumpfe, Jürgen Bajorath:
  MMP-Cliffs: Systematic Identification of Activity Cliffs on the Basis of Matched Molecular Pairs. 1138-1145

Computational Chemistry

• 
  Jean-Paul Ebejer, Garrett M. Morris, Charlotte M. Deane:
  Freely Available Conformer Generation Methods: How Good Are They? 1146-1158
• 
  Frederico Pratas, Leonel Sousa, Johannes M. Dieterich, Ricardo A. Mata:
  Computation of Induced Dipoles in Molecular Mechanics Simulations Using Graphics Processors. 1159-1166
• 
  Markus Hartenfeller, Martin Eberle, Peter Meier, Cristina Nieto-Oberhuber, Karl-Heinz Altmann, Gisbert Schneider, Edgar Jacoby, Steffen Renner:
  Probing the Bioactivity-Relevant Chemical Space of Robust Reactions and Common Molecular Building Blocks. 1167-1178
• 
  Jarmila Husby, Alan K. Todd, Shozeb M. Haider, Giovanna Zinzalla, David E. Thurston, Stephen Neidle:
  Molecular Dynamics Studies of the STAT3 Homodimer: DNA Complex: Relationships between STAT3 Mutations and Protein-DNA Recognition. 1179-1192
• 
  Nina Sadlej-Sosnowska, Aleksander P. Mazurek:
  Electron Density Distribution in Endohedral Complexes of Fullerene C₆₀, Calculated Based on the Gauss Law. 1193-1198
• 
  Junmei Wang, Tingjun Hou:
  Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations. 1199-1212
• 
  Gerald Zapata-Torres, Angelica Fierro, Sebastian Miranda-Rojas, Carlos Guajardo, Patricio Saez-Briones, J. Cristian Salgado, Cristian Celis-Barros:
  Influence of Protonation on Substrate and Inhibitor Interactions at the Active Site of Human Monoamine Oxidase-A. 1213-1221
• 
  L. Mark Hall, Lowell H. Hall, Tzipporah M. Kertesz, Dennis W. Hill, Thomas R. Sharp, Edward Z. Oblak, Ying W. Dong, David S. Wishart, Ming-Hui Chen, David F. Grant:
  Development of Ecom₅₀ and Retention Index Models for Nontargeted Metabolomics: Identification of 1, 3-Dicyclohexylurea in Human Serum by HPLC/Mass Spectrometry. 1222-1237

Computational Biochemistry

• 
  Anna Edberg, Daniel Soeria-Atmadja, Jonas Laurila Bergman, Fredrik Johansson, Mats G. Gustafsson, Ulf Hammerling:
  Assessing Relative Bioactivity of Chemical Substances Using Quantitative Molecular Network Topology Analysis. 1238-1249
• 
  Sushil Kumar Mishra, Jan Adam, Michaela Wimmerová, Jaroslav Koca:
  In Silico Mutagenesis and Docking Study of Ralstonia solanacearum RSL Lectin: Performance of Docking Software To Predict Saccharide Binding. 1250-1261
• 
  Oliver Korb, Tjelvar S. G. Olsson, Simon Bowden, Richard J. Hall, Marcel L. Verdonk, John W. Liebeschuetz, Jason C. Cole:
  Potential and Limitations of Ensemble Docking. 1262-1274
• 
  Arghya Barman, Rajeev Prabhakar:
  Protonation States of the Catalytic Dyad of β-Secretase (BACE1) in the Presence of Chemically Diverse Inhibitors: A Molecular Docking Study. 1275-1287
• 
  Sai Lakshmana Vankayala, Jacqueline C. Hargis, H. Lee Woodcock III:
  Unlocking the Binding and Reaction Mechanism of Hydroxyurea Substrates as Biological Nitric Oxide Donors. 1288-1297
• 
  Hector Figueroa, Durgaprasad Peddi, Joshua M. Osborne, Brenan M. Wilson, Ranadheer Reddy Pesaru, Balakrishna Kurva, Swathi Ramaraju, Maria C. Milletti, Deborah L. Heyl:
  Modeling the Interface between Islet Amyloid Polypeptide and Insulin-Based Aggregation Inhibitors: Correlation to Aggregation Kinetics and Membrane Damage. 1298-1307
• 
  Özlem Demir, Rommie E. Amaro:
  Elements of Nucleotide Specificity in the Trypanosoma brucei Mitochondrial RNA Editing Enzyme RET2. 1308-1318

Pharmaceutical Modeling

• 
  Alessandra Nurisso, Juan Bravo, Pierre-Alain Carrupt, Antoine Daina:
  Molecular Docking Using the Molecular Lipophilicity Potential as Hydrophobic Descriptor: Impact on GOLD Docking Performance. 1319-1327
• 
  Matthew A. Lardy, Laurie LeBrun, Drew Bullard, Charles Kissinger, Alberto Gobbi:
  Building a Three-Dimensional Model of CYP2C9 Inhibition Using the Autocorrelator: An Autonomous Model Generator. 1328-1336
• 
  María Gálvez-Llompart, Jorge Gálvez, Ramón García-Domenech, Lemont B. Kier:
  Modeling Drug-Induced Anorexia by Molecular Topology. 1337-1344
• 
  Kiran Mahasenan, Chenglong Li:
  Novel Inhibitor Discovery through Virtual Screening against Multiple Protein Conformations Generated via Ligand-Directed Modeling: A Maternal Embryonic Leucine Zipper Kinase Example. 1345-1355
• 
  Dane Huang, Qiong Gu, Hu Ge, Jiming Ye, Noeris K. Salam, Arnold T. Hagler, Hongzhuan Chen, Jun Xu:
  On the Value of Homology Models for Virtual Screening: Discovering hCXCR3 Antagonists by Pharmacophore-Based and Structure-Based Approaches. 1356-1366
• 
  Fung-Yi Chan, Marco A. C. Neves, Ning Sun, Man-Wah Tsang, Yun-Chung Leung, Tak-Hang Chan, Ruben Abagyan, Kwok-Yin Wong:
  Validation of the AmpC β-Lactamase Binding Site and Identification of Inhibitors with Novel Scaffolds. 1367-1375
• 
  Amit K. Gupta, Kanika Varshney, Anil K. Saxena:
  Toward the Identification of a Reliable 3D QSAR Pharmacophore Model for the CCK2 Receptor Antagonism. 1376-1390
• 
  Susanne von Grafenstein, Judit Mihaly-Bison, Gerhard Wolber, Valery N. Bochkov, Klaus R. Liedl, Daniela Schuster:
  Identification of Novel Liver X Receptor Activators by Structure-Based Modeling. 1391-1400

Bioinformatics

• 
  Praveen K. Madala, David P. Fairlie, Mikael Bodén:
  Matching Cavities in G Protein-Coupled Receptors to Infer Ligand-Binding Sites. 1401-1410

Errata

• 
  Xia Ning, Michael A. Walters, George Karypis:
  Improved Machine Learning Models for Predicting Selective Compounds. 1411

Volume 52, Number 6, June 2012

Perspectives

• 
  Alexandre Varnek, Igor I. Baskin:
  Machine Learning Methods for Property Prediction in Chemoinformatics: Quo Vadis? 1413-1437

Chemical Information

• 
  Eric J. Baede, Ernest den Bekker, Jan-Willem Boiten, Deborah Cronin, Rob van Gammeren, Jacob de Vlieg:
  Integrated Project Views: Decision Support Platform for Drug Discovery Project Teams. 1438-1449
• 
  Martin Weisel, Hans-Marcus Bitter, François Diederich, W. Venus So, Rama Kondru:
  PROLIX: Rapid Mining of Protein-Ligand Interactions in Large Crystal Structure Databases. 1450-1461
• 
  Michal Jamróz, Joanna E. Rode, Slawomir Ostrowski, Piotr Lipinski, Jan Cz. Dobrowolski:
  Chirality Measures of α-Amino Acids. 1462-1479
• 
  Christian Tyrchan, Jonas Boström, Fabrizio Giordanetto, Jon Winter, Sorel Muresan:
  Exploiting Structural Information in Patent Specifications for Key Compound Prediction. 1480-1489
• 
  Ye Hu, Norbert Furtmann, Michael Gütschow, Jürgen Bajorath:
  Systematic Identification and Classification of Three-Dimensional Activity Cliffs. 1490-1498

Computational Chemistry

• 
  Tanja Schulz-Gasch, Christin Schärfer, Wolfgang Guba, Matthias Rarey:
  TFD: Torsion Fingerprints As a New Measure To Compare Small Molecule Conformations. 1499-1512
• 
  Plamen N. Penchev, Klaus-Peter Schulz, Morton E. Munk:
  INFERCNMR: A ¹³C NMR Interpretive Library Search System. 1513-1528

Computational Biochemistry

• 
  Maria Safi, Ryan H. Lilien:
  Efficient a Priori Identification of Drug Resistant Mutations Using Dead-End Elimination and MM-PBSA. 1529-1541
• 
  Georgios Leonis, Zaneta Czyznikowska, Grigorios Megariotis, Heribert Reis, Manthos G. Papadopoulos:
  Computational Studies of Darunavir into HIV-1 Protease and DMPC Bilayer: Necessary Conditions for Effective Binding and the Role of the Flaps. 1542-1558
• 
  Xiao Zhu, Pedro E. M. Lopes, Jihyun Shim, Alexander D. MacKerell Jr.:
  Intrinsic Energy Landscapes of Amino Acid Side-Chains. 1559-1572
• 
  Urban Bren, Chris Oostenbrink:
  Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations. 1573-1582
• 
  Antonija Tomic, Miguel González, Sanja Tomic:
  The Large Scale Conformational Change of the Human DPP III-Substrate Prefers the "Closed" Form. 1583-1594
• 
  Jacopo Sgrignani, Alessandra Magistrato:
  Influence of the Membrane Lipophilic Environment on the Structure and on the Substrate Access/Egress Routes of the Human Aromatase Enzyme. A Computational Study. 1595-1606

Pharmaceutical Modeling

• 
  Marijn P. A. Sanders, Arménio Jorge Moura Barbosa, Barbara Zarzycka, Gerry A. F. Nicolaes, Jan P. G. Klomp, Jacob de Vlieg, Alberto Del Rio:
  Comparative Analysis of Pharmacophore Screening Tools. 1607-1620
• 
  Siegfried S. F. Leung, Jona Mijalkovic, Kenneth W. Borrelli, Matthew P. Jacobson:
  Testing Physical Models of Passive Membrane Permeation. 1621-1636
• 
  Jed Zaretzki, Patrik Rydberg, Charles Bergeron, Kristin P. Bennett, Lars Olsen, Curt M. Breneman:
  RS-Predictor Models Augmented with SMARTCyp Reactivities: Robust Metabolic Regioselectivity Predictions for Nine CYP Isozymes. 1637-1659
• 
  Bo-Han Su, Yi-shu Tu, Emilio Xavier Esposito, Yufeng J. Tseng:
  Predictive Toxicology Modeling: Protocols for Exploring hERG Classification and Tetrahymena pyriformis End Point Predictions. 1660-1673
• 
  Flavio Ballante, Rino Ragno:
  3-D QSAutogrid/R: An Alternative Procedure To Build 3-D QSAR Models. Methodologies and Applications. 1674-1685
• 
  Ines Filipa Martins, Ana L. Teixeira, Luis Pinheiro, André O. Falcão:
  A Bayesian Approach to in Silico Blood-Brain Barrier Penetration Modeling. 1686-1697
• 
  Ruifeng Liu, Jin Liu, Gregory J. Tawa, Anders Wallqvist:
  2D SMARTCyp Reactivity-Based Site of Metabolism Prediction for Major Drug-Metabolizing Cytochrome P450 Enzymes. 1698-1712

Volume 52, Number 7, July 2012

Chemical Information

• 
  Eelke van der Horst, Patricia Marqués-Gallego, Thea Mulder-Krieger, Jacobus van Veldhoven, Johannes W. Kruisselbrink, Alexander Aleman, Michael T. M. Emmerich, Johannes Brussee, Andreas Bender, Adriaan P. IJzerman:
  Multi-Objective Evolutionary Design of Adenosine Receptor Ligands. 1713-1721
• 
  Eduardo B. de Melo, Márcia M. C. Ferreira:
  Four-Dimensional Structure-Activity Relationship Model to Predict HIV-1 Integrase Strand Transfer Inhibition using LQTA-QSAR Methodology. 1722-1732
• 
  Ágnes Peragovics, Zoltán Simon, Ildikó Brandhuber, Balázs Jelinek, Péter Hári, Csaba Hetényi, Pál Czobor, András Málnási-Csizmadia:
  Contribution of 2D and 3D Structural Features of Drug Molecules in the Prediction of Drug Profile Matching. 1733-1744
• 
  Clara D. Christ, Matthias Zentgraf, Jan M. Kriegl:
  Mining Electronic Laboratory Notebooks: Analysis, Retrosynthesis, and Reaction Based Enumeration. 1745-1756
• 
  John J. Irwin, Teague Sterling, Michael M. Mysinger, Erin S. Bolstad, Ryan G. Coleman:
  ZINC: A Free Tool to Discover Chemistry for Biology. 1757-1768
• 
  Anne Mai Wassermann, Peter Haebel, Nils Weskamp, Jürgen Bajorath:
  SAR Matrices: Automated Extraction of Information-Rich SAR Tables from Large Compound Data Sets. 1769-1776
• 
  Mikko J. Vainio, Thierry Kogej, Florian Raubacher:
  Automated Recycling of Chemistry for Virtual Screening and Library Design. 1777-1786
• 
  Shawn Martin:
  Lattice Enumeration for Inverse Molecular Design Using the Signature Descriptor. 1787-1797
• 
  Hongmao Sun, Sampada Shahane, Menghang Xia, Christopher P. Austin, Ruili Huang:
  Structure Based Model for the Prediction of Phospholipidosis Induction Potential of Small Molecules. 1798-1805
• 
  Ye Hu, Jürgen Bajorath:
  Extending the Activity Cliff Concept: Structural Categorization of Activity Cliffs and Systematic Identification of Different Types of Cliffs in the ChEMBL Database. 1806-1811

Computational Chemistry

• 
  Chang Sun Kong, Wei Luo, Sergiu Arapan, Pierre Villars, Shuichi Iwata, Rajeev Ahuja, Krishna Rajan:
  Information-Theoretic Approach for the Discovery of Design Rules for Crystal Chemistry. 1812-1820
• 
  Hui Sun Lee, Sunhwan Jo, Hyun-Suk Lim, Wonpil Im:
  Application of Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors. 1821-1832
• 
  Ding Li, Jie Gui, Yongjian Li, Lingling Feng, Xinya Han, Yao Sun, Tinglin Sun, Zhigang Chen, Yi Cao, Yang Zhang, Li Zhou, Xiaopeng Hu, Yanliang Ren, Jian Wan:
  Structure-Based Design and Screen of Novel Inhibitors for Class II 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase from Streptococcus Pneumoniae. 1833-1841

Computational Biochemistry

• 
  James A. R. Dalton, Ori Kalid, Maya Schushan, Nir Ben-Tal, Jordi Villà-Freixa:
  New Model of Cystic Fibrosis Transmembrane Conductance Regulator Proposes Active Channel-like Conformation. 1842-1853
• 
  Svetoslav H. Slavov, Elizabeth L. Geesaman, Bruce A. Pearce, Laura K. Schnackenberg, Dan A. Buzatu, Jon G. Wilkes, Richard D. Beger:
  ¹³C NMR-Distance Matrix Descriptors: Optimal Abstract 3D Space Granularity for Predicting Estrogen Binding. 1854-1864
• 
  Marco Pasi, Matteo Tiberti, Alberto Arrigoni, Elena Papaleo:
  xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures. 1865-1874
• 
  Jun Tan, Ravinder Abrol, Bartosz Trzaskowski, William A. Goddard III:
  3D Structure Prediction of TAS2R38 Bitter Receptors Bound to Agonists Phenylthiocarbamide (PTC) and 6-n-Propylthiouracil (PROP). 1875-1885

Pharmaceutical Modeling

• 
  Ting-Lan Chiu, Elizabeth A. Amin:
  Development of a Comprehensive, Validated Pharmacophore Hypothesis for Anthrax Toxin Lethal Factor (LF) Inhibitors Using Genetic Algorithms, Pareto Scoring, and Structural Biology. 1886-1897

Computer Software Reviews

• 
  Eugene E. Kwan:
  ACD/Spectrus Processor Review. 1898-1900

Volume 52, Number 8, August 2012

Chemical Information

• 
  Nick Spadaccini, Sydney R. Hall:
  Extensions to the STAR File Syntax. 1901-1906
• 
  Nick Spadaccini, Sydney R. Hall:
  DDLm: A New Dictionary Definition Language. 1907-1916
• 
  Nick Spadaccini, Ian R. Castleden, Douglas du Boulay, Sydney R. Hall:
  dREL: A Relational Expression Language for Dictionary Methods. 1917-1925
• 
  David Tai, Jianwen Fang:
  SymDex: Increasing the Efficiency of Chemical Fingerprint Similarity Searches for Comparing Large Chemical Libraries by Using Query Set Indexing. 1926-1935
• 
  David A. Cosgrove, Keith M. Green, Andrew Leach, Andrew R. Poirrette, Jon Winter:
  A System for Encoding and Searching Markush Structures. 1936-1947
• 
  Violeta I. Pérez-Nueno, Vishwesh Venkatraman, Lazaros Mavridis, David W. Ritchie:
  Detecting Drug Promiscuity Using Gaussian Ensemble Screening. 1948-1961
• 
  Preeti Iyer, Dilyana Dimova, Martin Vogt, Jürgen Bajorath:
  Navigating High-Dimensional Activity Landscapes: Design and Application of the Ligand-Target Differentiation Map. 1962-1969
• 
  Paulo J. Mendes, Tiago J. L. Silva, M. Helena Garcia, J. P. Prates Ramalho, A. J. Palace Carvalho:
  Switchable Nonlinear Optical Properties of η⁵-Monocyclopentadienylmetal Complexes: A DFT Approach. 1970-1983
• 
  Manuel Hechinger, Kai Leonhard, Wolfgang Marquardt:
  What is Wrong with Quantitative Structure-Property Relations Models Based on Three-Dimensional Descriptors? 1984-1993
• 
  Yong Wang, Jing Lu, Fei Wang, Qiancheng Shen, Mingyue Zheng, Xiaomin Luo, Weiliang Zhu, Hualiang Jiang, Kaixian Chen:
  Estimation of Carcinogenicity Using Molecular Fragments Tree. 1994-2003

Computational Chemistry

• 
  Sarath Kumar Baskaran, Nabajyoti Goswami, Sudhagar Selvaraj, Velusamy Shanmuganathan Muthusamy, Baddireddi Subhadra Lakshmi:
  Molecular Dynamics Approach to Probe the Allosteric Inhibition of PTP1B by Chlorogenic and Cichoric Acid. 2004-2012
• 
  Adrian Kolodzik, Sascha Urbaczek, Matthias Rarey:
  Unique Ring Families: A Chemically Meaningful Description of Molecular Ring Topologies. 2013-2021
• 
  Thomas Klabunde, Clemens Giegerich, Andreas Evers:
  MARS: Computing Three-Dimensional Alignments for Multiple Ligands Using Pairwise Similarities. 2022-2030
• 
  David J. Wood, Jacob de Vlieg, Markus Wagener, Tina Ritschel:
  Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement. 2031-2043
• 
  Nicola Chirico, Paola Gramatica:
  Real External Predictivity of QSAR Models. Part 2. New Intercomparable Thresholds for Different Validation Criteria and the Need for Scatter Plot Inspection. 2044-2058
• 
  Megumi Ikemori-Kawada, Atsushi Inoue, Masaki Goto, Yuan John Wang, Yoshiyuki Kawakami:
  Docking Simulation Study and Kinase Selectivity of f152A1 and Its Analogs. 2059-2068
• 
  Giuliano Berellini, Nigel J. Waters, Franco Lombardo:
  In silico Prediction of Total Human Plasma Clearance. 2069-2078
• 
  Samuel Genheden, Oliver Kuhn, Paulius Mikulskis, Daniel Hoffmann, Ulf Ryde:
  The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant. 2079-2088

Computational Biochemistry

• 
  Alexey Ishchenko, Zhijie Liu, Peter Lindblom, Guosheng Wu, Kam-Chuen Jim, Richard D. Gregg, David A. Claremon, Suresh B. Singh:
  Structure-Based Design Technology Contour and Its Application to the Design of Renin Inhibitors. 2089-2097
• 
  Richard D. Smith, Alaina L. Engdahl, James B. Dunbar Jr., Heather A. Carlson:
  Biophysical Limits of Protein-Ligand Binding. 2098-2106
• 
  Laura Delgado-Soler, Marta Pinto, Kaori Tanaka-Gil, Jaime Rubio-Martinez:
  Molecular Determinants of Bim(BH3) Peptide Binding to Pro-Survival Proteins. 2107-2118
• 
  Zhiwei Feng, Tingjun Hou, Youyong Li:
  Concerted Movement in pH-Dependent Gating of FocA from Molecular Dynamics Simulations. 2119-2131
• 
  Jian Liu, Jianfen Fan, Min Cen, Xuezeng Song, Dongyan Liu, Weiqun Zhou, Zhao Liu, Jianfeng Yan:
  Dependences of Water Permeation through Cyclic Octa-peptide Nanotubes on Channel Length and Membrane Thickness. 2132-2138
• 
  Stephanie B. A. De Beer, Harini Venkataraman, Daan P. Geerke, Chris Oostenbrink, Nico P. E. Vermeulen:
  Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants. 2139-2148

Pharmaceutical Modeling

• 
  Michael Thormann, Andreas Klamt, Karin Wichmann:
  COSMOsim3D: 3D-Similarity and Alignment Based on COSMO Polarization Charge Densities. 2149-2156
• 
  Andreas Klamt, Michael Thormann, Karin Wichmann, Paolo Tosco:
  COSMOsar3D: Molecular Field Analysis Based on Local COSMO σ-Profiles. 2157-2164
• 
  Alfonso T. García-Sosa, Mare Oja, Csaba Hetényi, Uko Maran:
  DrugLogit: Logistic Discrimination between Drugs and Nondrugs Including Disease-Specificity by Assigning Probabilities Based on Molecular Properties. 2165-2180
• 
  Rajarshi Guha:
  Exploring Uncharted Territories: Predicting Activity Clis in Structure-Activity Landscapes. 2181-2191
• 
  Daniel N. Santiago, Yuri Pevzner, Ashley A. Durand, Minh Phuong Tran, Rachel R. Scheerer, Kenyon G. Daniel, Shen-Shu Sung, H. Lee Woodcock III, Wayne C. Guida, Wesley H. Brooks:
  Virtual Target Screening: Validation Using Kinase Inhibitors. 2192-2203
• 
  Michael Oberlin, Romano T. Kroemer, Vincent Mikol, Hervé Minoux, Erdogan Tastan, Nicolas Baurin:
  Engineering Protein Therapeutics: Predictive Performances of a Structure-Based Virtual Affinity Maturation Protocol. 2204-2214
• 
  Laura Silvestri, Flavio Ballante, Antonello Mai, Garland R. Marshall, Rino Ragno:
  Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction. 2215-2235
• 
  Brandon S. Zerbe, David R. Hall, Sandor Vajda, Adrian Whitty, Dima Kozakov:
  Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces. 2236-2244
• 
  Rima Chaudhuri, Hyun Lee, Lena Truong, Jaime Torres, Kavankumar Patel, Michael E. Johnson:
  Identification of Non-Macrocyclic Small Molecule Inhibitors against the NS3/4A Serine Protease of Hepatitis C Virus through in Silico Screening. 2245-2256
• 
  Naoya Nagata, Kentaro Kawai, Isao Nakanishi:
  Subtle Structural Changes in Tetrahydroquinolines, A New Class of Nonsteroidal Selective Androgen Receptor Modulators, Induce Different Functions. 2257-2264
• 
  Sandra Dreisigacker, Dorota Latek, Svenja Bockelmann, Markus Huss, Helmut Wieczorek, Slawomir Filipek, Holger Gohlke, Dirk Menche, Teresa Carlomagno:
  Understanding the Inhibitory Effect of Highly Potent and Selective Archazolides Binding to the Vacuolar ATPase. 2265-2272

Bioinformatics

• 
  Billur Engin, Ozlem Keskin, Ruth Nussinov, Attila Gürsoy:
  A Strategy Based on Protein-Protein Interface Motifs May Help in Identifying Drug Off-Targets. 2273-2286

Software Description

• 
  Jérémy Desaphy, Karima Azdimousa, Esther Kellenberger, Didier Rognan:
  Comparison and Druggability Prediction of Protein-Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes. 2287-2299
• 
  Álvaro Cortés Cabrera, Javier Klett, Helena G. Dos Santos, Almudena Perona, Rubén Gil-Redondo, Sandrea M. Francis, Eva-Maria Priego, Federico Gago, Antonio Morreale:
  CRDOCK: An Ultrafast Multipurpose Protein-Ligand Docking Tool. 2300-2309
• 
  Iurii Sushko, Elena Salmina, Vladimir Potemkin, Gennadiy Poda, Igor V. Tetko:
  ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions. 2310-2316

Errata

• 
  Xiao Zhu, Pedro E. M. Lopes, Jihyun Shim, Alexander D. MacKerell Jr.:
  Correction to Intrinsic Energy Landscapes of Amino Acid Side-Chains. 2317-2318

Volume 52, Number 9, September 2012

Letters

• 
  Weizhuang Zhou, Efthimios Motakis, Gloria Fuentes, Chandra S. Verma:
  Macrostate Identification from Biomolecular Simulations through Time Series Analysis. 2319-2324

Chemical Information

• 
  Aurélie de Luca, Dragos Horvath, Gilles Marcou, Vitaly P. Solov'ev, Alexandre Varnek:
  Mining Chemical Reactions Using Neighborhood Behavior and Condensed Graphs of Reactions Approaches. 2325-2338
• 
  Britta Nisius, Holger Gohlke:
  Alignment-Independent Comparison of Binding Sites Based on DrugScore Potential Fields Encoded by 3D Zernike Descriptors. 2339-2347
• 
  Dagmar Stumpfe, Jürgen Bajorath:
  Frequency of Occurrence and Potency Range Distribution of Activity Cliffs in Bioactive Compounds. 2348-2353
• 
  Kathrin Heikamp, Xiaoying Hu, Aixia Yan, Jürgen Bajorath:
  Prediction of Activity Cliffs Using Support Vector Machines. 2354-2365

Computational Chemistry

• 
  Yunierkis Pérez-Castillo, Cosmin Lazar, Jonatan Taminau, Matheus Froeyen, Miguel Ángel Cabrera-Pérez, Ann Nowé:
  GA(M)E-QSAR: A Novel, Fully Automatic Genetic-Algorithm-(Meta)-Ensembles Approach for Binary Classification in Ligand-Based Drug Design. 2366-2386
• 
  Fernando Blanco, Billy Egan, Laura Caboni, José Elguero, John O'Brien, Thomas McCabe, Darren Fayne, Mary J. Meegan, David G. Lloyd:
  Study of E/Z Isomerization in a Series of Novel Non-ligand Binding Pocket Androgen Receptor Antagonists. 2387-2397

Computational Biochemistry

• 
  Shaoyong Lu, Wenkang Huang, Xiaobai Li, Zhimin Huang, Xinyi Liu, Yingyi Chen, Ting Shi, Jian Zhang:
  Insights into the Role of Magnesium Triad in myo-Inositol Monophosphatase: Metal Mechanism, Substrate Binding, and Lithium Therapy. 2398-2409
• 
  Noé Sturm, Jérémy Desaphy, Ronald J. Quinn, Didier Rognan, Esther Kellenberger:
  Structural Insights into the Molecular Basis of the Ligand Promiscuity. 2410-2421
• 
  Ying Wang, Xiaolin Wu, Dong-Qing Wei, Yi-Xue Li, Jing-Fang Wang:
  Autoinhibitory Mechanism for the Mutation-Induced Impaired FGF9 Signaling. 2422-2429

Pharmaceutical Modeling

• 
  Prasenjit Mukherjee, Eric J. Martin:
  Profile-QSAR and Surrogate AutoShim Protein-Family Modeling of Proteases. 2430-2440
• 
  Stefan Güssregen, Hans Matter, Gerhard Hessler, Marco Müller, K. Friedemann Schmidt, Timothy Clark:
  3D-QSAR Based on Quantum-Chemical Molecular Fields: Toward an Improved Description of Halogen Interactions. 2441-2453
• 
  Austin B. Yongye, José L. Medina-Franco:
  Data Mining of Protein-Binding Profiling Data Identifies Structural Modifications that Distinguish Selective and Promiscuous Compounds. 2454-2461
• 
  Fabio Broccatelli:
  QSAR Models for P-Glycoprotein Transport Based on a Highly Consistent Data Set. 2462-2470
• 
  Valérie Campagna-Slater, Joshua Pottel, Eric Therrien, Louis-David Cantin, Nicolas Moitessier:
  Development of a Computational Tool to Rival Experts in the Prediction of Sites of Metabolism of Xenobiotics by P450s. 2471-2483

Errata

• 
  Svetoslav H. Slavov, Elizabeth L. Geesaman, Bruce A. Pearce, Laura K. Schnackenberg, Dan A. Buzatu, Jon G. Wilkes, Richard D. Beger:
  Erratum: ¹³C NMR - Distance Matrix Descriptors: Optimal Abstract 3D Space Granularity for Predicting Estrogen Binding. 2484

Volume 52, Number 10, October 2012

Perspectives

• 
  José L. Medina-Franco:
  Scanning Structure-Activity Relationships with Structure-Activity Similarity and Related Maps: From Consensus Activity Cliffs to Selectivity Switches. 2485-2493

Chemical Information

• 
  Joe Townsend, Robert C. Glen, Hamse Y. Mussa:
  Note on Naive Bayes Based on Binary Descriptors in Cheminformatics. 2494-2500
• 
  Anshuman Dixit, Gennady Verkhivker:
  Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations. 2501-2515
• 
  Nicholas C. Firth, Nathan Brown, Julian Blagg:
  Plane of Best Fit: A Novel Method to Characterize the Three-Dimensionality of Molecules. 2516-2525
• 
  Matthew A. Kayala, Pierre Baldi:
  ReactionPredictor: Prediction of Complex Chemical Reactions at the Mechanistic Level Using Machine Learning. 2526-2540
• 
  Nejc Carl, Milan Hodoscek, Blaz Vehar, Janez Konc, Bernard R. Brooks, Dusanka Janezic:
  Correlating Protein Hot Spot Surface Analysis Using ProBiS with Simulated Free Energies of Protein-Protein Interfacial Residues. 2541-2549
• 
  Ye Hu, Jürgen Bajorath:
  Growth of Ligand-Target Interaction Data in ChEMBL Is Associated with Increasing and Activity Measurement-Dependent Compound Promiscuity. 2550-2558
• 
  Narender Singh, Sidhartha Chaudhury, Ruifeng Liu, Mohamed Diwan M. AbdulHameed, Gregory J. Tawa, Anders Wallqvist:
  QSAR Classification Model for Antibacterial Compounds and Its Use in Virtual Screening. 2559-2569
• 
  Todd Martin, Paul Harten, Douglas M. Young, Eugene N. Muratov, Alexander Golbraikh, Hao Zhu, Alexander Tropsha:
  Does Rational Selection of Training and Test Sets Improve the Outcome of QSAR Modeling? 2570-2578
• 
  Disha Gupta-Ostermann, Jürgen Bajorath:
  Identification of Multitarget Activity Ridges in High-Dimensional Bioactivity Spaces. 2579-2586

Computational Chemistry

• 
  Simon Cross, Massimo Baroni, Laura Goracci, Gabriele Cruciani:
  GRID-Based Three-Dimensional Pharmacophores I: FLAPpharm, a Novel Approach for Pharmacophore Elucidation. 2587-2598
• 
  Simon Cross, Francesco Ortuso, Massimo Baroni, Giosuè Costa, Simona Distinto, Federica Moraca, Stefano Alcaro, Gabriele Cruciani:
  GRID-Based Three-Dimensional Pharmacophores II: PharmBench, a Benchmark Data Set for Evaluating Pharmacophore Elucidation Methods. 2599-2608
• 
  Suman K. Chakravarti, Roustem D. Saiakhov, Gilles Klopman:
  Optimizing Predictive Performance of CASE Ultra Expert System Models Using the Applicability Domains of Individual Toxicity Alerts. 2609-2618
• 
  Maninder Kaur, Malkeet Singh Bahia, Om Silakari:
  Exploring the Role of Water Molecules for Docking and Receptor Guided 3D-QSAR Analysis of Naphthyridine Derivatives as Spleen Tyrosine Kinase (Syk) Inhibitors. 2619-2630
• 
  Patricia Saenz-Méndez, Ali Ateia Elmabsout, Helena Sävenstrand, Mohamed Khalid Alhaj Awadalla, Åke Strid, Allan Sirsjö, Leif A. Eriksson:
  Homology Models of Human All-Trans Retinoic Acid Metabolizing Enzymes CYP26B1 and CYP26B1 Spliced Variant. 2631-2637
• 
  Abhishek Singharoy, Harshad Joshi, Peter J. Ortoleva:
  Multiscale Macromolecular Simulation: Role of Evolving Ensembles. 2638-2649
• 
  Ariela Vergara Jaque, Horacio Poblete, Eric H. Lee, Klaus Schulten, Fernando D. González Nilo, Christophe Chipot:
  Molecular Basis of Drug Resistance in A/H1N1 Virus. 2650-2656

Computational Biochemistry

• 
  Thomas H. Schmidt, Christian Kandt:
  LAMBADA and InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations. 2657-2669
• 
  Eleonora Gianti, Randy J. Zauhar:
  Modeling Androgen Receptor Flexibility: A Binding Mode Hypothesis of CYP17 Inhibitors/Antiandrogens for Prostate Cancer Therapy. 2670-2683
• 
  Wanding Zhou, Luay Nakhleh:
  Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic Pathways. 2684-2696
• 
  Sandro Cosconati, Luciana Marinelli, Francesco Saverio Di Leva, Valeria La Pietra, Angela De Simone, Francesca Mancini, Vincenza Andrisano, Ettore Novellino, David S. Goodsell, Arthur J. Olson:
  Protein Flexibility in Virtual Screening: The BACE-1 Case Study. 2697-2704

Pharmaceutical Modeling

• 
  Manuel Rueda, Maxim Totrov, Ruben Abagyan:
  ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader. 2705-2714
• 
  Lin Li, Youyong Li, Liling Zhang, Tingjun Hou:
  Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase. 2715-2729
• 
  Ran Cao, Minyu Liu, Min Yin, Quanhai Liu, Yanli Wang, Niu Huang:
  Discovery of Novel Tubulin Inhibitors via Structure-Based Hierarchical Virtual Screening. 2730-2740
• 
  Lu Chen, George A. Calin, Shuxing Zhang:
  Novel Insights of Structure-Based Modeling for RNA-Targeted Drug Discovery. 2741-2753
• 
  Njabulo J. Gumede, Parvesh Singh, Myalowenkosy I. Sabela, Krishna Bisetty, Laura Escuder-Gilabert, María-José Medina-Hernández, Salvador Sagrado:
  Experimental-Like Affinity Constants and Enantioselectivity Estimates from Flexible Docking. 2754-2759
• 
  Serdar Durdagi, Sumukh Deshpande, Henry J. Duff, Sergei Yu Noskov:
  Modeling of Open, Closed, and Open-Inactivated States of the hERG1 Channel: Structural Mechanisms of the State-Dependent Drug Binding. 2760-2774

Bioinformatics

• 
  Nelson Alberto N. de Alencar, Paulo Robson M. Sousa, José Rogério A. Silva, Jerônimo Lameira, Cláudio Nahum Alves, Sergio Martí, Vicent Moliner:
  Computational Analysis of Human OGA Structure in Complex with PUGNAc and NAG-Thiazoline Derivatives. 2775-2783
• 
  Hui Sun Lee, Wonpil Im:
  Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design. 2784-2795

Software Description

• 
  Tianhong Zhang, Hongli Li, Hualin Xi, Robert V. Stanton, Sergio H. Rotstein:
  HELM: A Hierarchical Notation Language for Complex Biomolecule Structure Representation. 2796-2806

Volume 52, Number 11, November 2012

Letters

• 
  Dennis M. Krüger, Gisela Jessen, Holger Gohlke:
  How Good Are State-of-the-Art Docking Tools in Predicting Ligand Binding Modes in Protein-Protein Interfaces? 2807-2811

Chemical Information

• 
  Ksenia S. Egorova, Philip V. Toukach:
  Critical Analysis of CCSD Data Quality. 2812-2814
• 
  Ulf Norinder, Henrik Boström:
  Introducing Uncertainty in Predictive Modeling - Friend or Foe? 2815-2822
• 
  Amol Shivajirao Hukkerikar, Sawitree Kalakul, Bent Sarup, Douglas M. Young, Gürkan Sin, Rafiqul Gani:
  Estimation of Environment-Related Properties of Chemicals for Design of Sustainable Processes: Development of Group-Contribution⁺ (GC⁺) Property Models and Uncertainty Analysis. 2823-2839
• 
  Congying Xu, Feixiong Cheng, Lei Chen, Zheng Du, Weihua Li, Guixia Liu, Philip W. Lee, Yun Tang:
  In silico Prediction of Chemical Ames Mutagenicity. 2840-2847
• 
  Vigneshwaran Namasivayam, Jürgen Bajorath:
  Multiobjective Particle Swarm Optimization: Automated Identification of Structure-Activity Relationship-Informative Compounds with Favorable Physicochemical Property Distributions. 2848-2855
• 
  Alexandru T. Balaban:
  Partitioned-Formula Periodic Tables for Diamond Hydrocarbons (Diamondoids). 2856-2863
• 
  Lars Ruddigkeit, Ruud van Deursen, Lorenz C. Blum, Jean-Louis Reymond:
  Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17. 2864-2875
• 
  Antonio de la Vega de León, Jürgen Bajorath:
  Design of a Three-Dimensional Multitarget Activity Landscape. 2876-2883

Computational Chemistry

• 
  Roberto Todeschini, Viviana Consonni, Hua Xiang, John D. Holliday, Paolo Massimo Buscema, Peter Willett:
  Similarity Coefficients for Binary Chemoinformatics Data: Overview and Extended Comparison Using Simulated and Real Data Sets. 2884-2901
• 
  Maciej Haranczyk, Piotr Urbaszek, Esmond G. Ng, Tomasz Puzyn:
  Combinatorial × Computational × Cheminformatics (C³) Approach to Characterization of Congeneric Libraries of Organic Pollutants. 2902-2909
• 
  Gunnar Brinkmann, Jan Goedgebeur, Brendan D. McKay:
  The Generation of Fullerenes. 2910-2918
• 
  Paul C. D. Hawkins, Anthony Nicholls:
  Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures. 2919-2936
• 
  Gregory A. Bakken, Andrew Bell, Markus Boehm, Jeremy R. Everett, Rosalia Gonzales, David Hepworth, Jacquelyn L. Klug-McLeod, Jeremy Lanfear, Jens Loesel, John Mathias, Terence P. Wood:
  Shaping a Screening File for Maximal Lead Discovery Efficiency and Effectiveness: Elimination of Molecular Redundancy. 2937-2949
• 
  Jogoth Ali, Patrick Camilleri, Marc B. Brown, Andrew J. Hutt, Stewart B. Kirton:
  In Silico Prediction of Aqueous Solubility Using Simple QSPR Models: The Importance of Phenol and Phenol-like Moieties. 2950-2957

Computational Biochemistry

• 
  R. S. K. Vijayan, Neha Trivedi, Sudipendra Nath Roy, Indrani Bera, Prabu Manoharan, Pavan V. Payghan, Dhananjay Bhattacharyya, Nanda Ghoshal:
  Modeling the Closed and Open State Conformations of the GABA_A Ion Channel - Plausible Structural Insights for Channel Gating. 2958-2969
• 
  Mario Latendresse, Jeremiah P. Malerich, Mike Travers, Peter D. Karp:
  Accurate Atom-Mapping Computation for Biochemical Reactions. 2970-2982
• 
  Yiyu Li, Mámon M. Hatmal, Ralf Langen, Ian S. Haworth:
  Idealized Models of Protofilaments of Human Islet Amyloid Polypeptide. 2983-2991
• 
  Shunzhou Wan, Peter V. Coveney:
  Regulation of JAK2 Activation by Janus Homology 2: Evidence from Molecular Dynamics Simulations. 2992-3000
• 
  Bruno L. Victor, António M. Baptista, Cláudio M. Soares:
  Structural Determinants for the Membrane Insertion of the Transmembrane Peptide of Hemagglutinin from Influenza Virus. 3001-3012
• 
  Samuel Genheden:
  Are Homology Models Sufficiently Good for Free-Energy Simulations? 3013-3021
• 
  Maxime Louet, Landry Charlier, Jean Martinez, Nicolas Floquet:
  Dissociation of Membrane-Anchored Heterotrimeric G-Protein Induced by G_α Subunit Binding to GTP. 3022-3027
• 
  Niels Johan Christensen, Kasper P. Kepp:
  Accurate Stabilities of Laccase Mutants Predicted with a Modified FoldX Protocol. 3028-3042
• 
  Weihua Li, Jing Fu, Feixiong Cheng, Mingyue Zheng, Jian Zhang, Guixia Liu, Yun Tang:
  Unbinding Pathways of GW4064 from Human Farnesoid X Receptor As Revealed by Molecular Dynamics Simulations. 3043-3052
• 
  Sabina Berne, Barbara Podobnik, Neja Zupanec, Metka Novak, Nada Krasevec, Samo Turk, Branka Korosec, Ljerka Lah, Erika Suligoj, Jure Stojan, Stanislav Gobec, Radovan Komel:
  Virtual Screening Yields Inhibitors of Novel Antifungal Drug Target, Benzoate 4-Monooxygenase. 3053-3063

Pharmaceutical Modeling

• 
  Yunde Xiao, Philip S. Hammond, Anatoly A. Mazurov, Daniel Yohannes:
  Multiple Interaction Regions in the Orthosteric Ligand Binding Domain of the α7 Neuronal Nicotinic Acetylcholine Receptor. 3064-3073
• 
  Richard Sherhod, Valerie J. Gillet, Philip N. Judson, Jonathan D. Vessey:
  Automating Knowledge Discovery for Toxicity Prediction Using Jumping Emerging Pattern Mining. 3074-3087
• 
  Hemant Kumar Srivastava, G. Narahari Sastry:
  Molecular Dynamics Investigation on a Series of HIV Protease Inhibitors: Assessing the Performance of MM-PBSA and MM-GBSA Approaches. 3088-3098

Software Description

• 
  Feixiong Cheng, Weihua Li, Yadi Zhou, Jie Shen, Zengrui Wu, Guixia Liu, Philip W. Lee, Yun Tang:
  admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties. 3099-3105

Volume 52, Number 12, December 2012

Chemical Information

• 
  Dusica Vidovic, Steven M. Muskal, Stephan C. Schürer:
  Novel Kinase Inhibitors by Reshuffling Ligand Functionalities Across the Human Kinome. 3107-3115
• 
  Christophe Muller, Gilles Marcou, Dragos Horvath, João Aires-de-Sousa, Alexandre Varnek:
  Models for Identification of Erroneous Atom-to-Atom Mapping of Reactions Performed by Automated Algorithms. 3116-3122
• 
  Obdulia Rabal, Julen Oyarzabal:
  Biologically Relevant Chemical Space Navigator: From Patent and Structure-Activity Relationship Analysis to Library Acquisition and Design. 3123-3137
• 
  Bijun Zhang, Anne Mai Wassermann, Martin Vogt, Jürgen Bajorath:
  Systematic Assessment of Compound Series with SAR Transfer Potential. 3138-3143

Computational Chemistry

• 
  Kenno Vanommeslaeghe, Alexander D. MacKerell Jr.:
  Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing. 3144-3154
• 
  Kenno Vanommeslaeghe, E. Prabhu Raman, Alexander D. MacKerell Jr.:
  Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges. 3155-3168
• 
  Yan Yuan, Hugh A. Chipman, William J. Welch:
  Harvesting Classification Trees for Drug Discovery. 3169-3180
• 
  Hans-Christian Ehrlich, Andrea Volkamer, Matthias Rarey:
  Searching for Substructures in Fragment Spaces. 3181-3189
• 
  Haipeng Hu, James P. Snyder:
  Models for Predicting IKKA and IKKB Blockade. 3190-3199
• 
  Miklos Feher, Christopher I. Williams:
  Numerical Errors in Minimization Based Binding Energy Calculations. 3200-3212
• 
  Dima A. Sabbah, Jonathan L. Vennerstrom, Haizhen Zhong:
  Binding Selectivity Studies of Phosphoinositide 3-Kinases Using Free Energy Calculations. 3213-3224
• 
  Woong-Hee Shin, Chaok Seok:
  GalaxyDock: Protein-Ligand Docking with Flexible Protein Side-chains. 3225-3232
• 
  Paola Bisignano, Chiara Lambruschini, Manuele Bicego, Vittorio Murino, Angelo D. Favia, Andrea Cavalli:
  In Silico Deconstruction of ATP-Competitive Inhibitors of Glycogen Synthase Kinase-3β. 3233-3244
• 
  Laura De Luca, Francesca Morreale, Alba Chimirri:
  Insight into the Fundamental Interactions between LEDGF Binding Site Inhibitors and Integrase Combining Docking and Molecular Dynamics Simulations. 3245-3254
• 
  Jack Yang, Mark P. Waller:
  JACOB: A Dynamic Database for Computational Chemistry Benchmarking. 3255-3262
• 
  Thijs Beuming, Woody Sherman:
  Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines. 3263-3277

Computational Biochemistry

• 
  Minsup Kim, Keun Woo Lee, Art E. Cho:
  Elucidation of Allosteric Inhibition Mechanism of 2-Cys Human Peroxiredoxin by Molecular Modeling. 3278-3283

Pharmaceutical Modeling

• 
  Yoshihiro Yamanishi, Edouard Pauwels, Masaaki Kotera:
  Drug Side-Effect Prediction Based on the Integration of Chemical and Biological Spaces. 3284-3292
• 
  Eleni Vrontaki, Georgios Leonis, Manthos G. Papadopoulos, M. Simcic, Simona Golic Grdadolnik, Antreas Afantitis, Georgia Melagraki, S. K. Hadjikakou, Thomas M. Mavromoustakos:
  Comparative Binding Effects of Aspirin and Anti-Inflammatory Cu Complex in the Active Site of LOX-1. 3293-3301
• 
  Anthony F. Nastase, Donald B. Boyd:
  Simple Structure-Based Approach for Predicting the Activity of Inhibitors of Beta-Secretase (BACE1) Associated with Alzheimer's Disease. 3302-3307
• 
  Francesco Sirci, Enade P. Istyastono, Henry F. Vischer, Albert J. Kooistra, Saskia Nijmeijer, Martien Kuijer, Maikel Wijtmans, Raimund Mannhold, Rob Leurs, Iwan J. P. de Esch, Chris de Graaf:
  Virtual Fragment Screening: Discovery of Histamine H₃ Receptor Ligands Using Ligand-Based and Protein-Based Molecular Fingerprints. 3308-3324
• 
  Mauricio E. Di Ianni, Andrea V. Enrique, Pablo H. Palestro, Luciana Gavernet, Alan Talevi, Luis Bruno Blanch:
  Several New Diverse Anticonvulsant Agents Discovered in a Virtual Screening Campaign Aimed at Novel Antiepileptic Drugs to Treat Refractory Epilepsy. 3325-3330

Bioinformatics

• 
  Humberto González Díaz, Pablo Riera-Fernández:
  New Markov-Autocorrelation Indices for Re-evaluation of Links in Chemical and Biological Complex Networks used in Metabolomics, Parasitology, Neurosciences, and Epidemiology. 3331-3340
• 
  Nédia Kamech, Damir Vukicevic, Ali Ladram, Christophe Piesse, Julie Vasseur, Viktor Bojovic, Juraj Simunic, Davor Juretic:
  Improving the Selectivity of Antimicrobial Peptides from Anuran Skin. 3341-3351