Journal of Chemical Information and Modeling, Volume 49

Volume 49, Number 1, January 2009

Letter

• 
  Anton J. Hopfinger, Emilio Xavier Esposito, Antonio Llinàs, Robert C. Glen, Jonathan M. Goodman:
  Findings of the Challenge To Predict Aqueous Solubility. 1-5

Chemical Information

• 
  Felix Reisen, Gisbert Schneider, Ewgenij Proschak:
  Reaction-MQL: Line Notation for Functional Transformation. 6-12
• 
  Yevgeniy Podolyan, George Karypis:
  Common Pharmacophore Identification Using Frequent Clique Detection Algorithm. 13-21
• 
  Adel Golovin, Kim Henrick:
  Chemical Substructure Search in SQL. 22-27
• 
  Christian Kramer, Christofer S. Tautermann, David J. Livingstone, David W. Salt, David C. Whitley, Bernd Beck, Timothy Clark:
  Sharpening the Toolbox of Computational Chemistry: A New Approximation of Critical F-Values for Multiple Linear Regression. 28-34
• 
  Ashutosh Kumar, Vinita Chaturvedi, Shalini Bhatnagar, Sudhir Sinha, Mohammad Imran Siddiqi:
  Knowledge Based Identification of Potent Antitubercular Compounds Using Structure Based Virtual Screening and Structure Interaction Fingerprints. 35-42

Computational Chemistry

• 
  Poongavanam Vasanthanathan, Jozef Hritz, Olivier Taboureau, Lars Olsen, Flemming Steen Jørgensen, Nico P. E. Vermeulen, Chris Oostenbrink:
  Virtual Screening and Prediction of Site of Metabolism for Cytochrome P450 1A2 Ligands. 43-52
• 
  Ravi Shashi Nayana, Suneel Kumar Bommisetty, Kriti Singh, Santhosh Kumar Bairy, Sivakumari Nunna, Akula Pramod, Ravikumar Muttineni:
  Structural Analysis of Carboline Derivatives As Inhibitors of MAPKAP K2 Using 3D QSAR and Docking Studies. 53-67
• 
  Francesca Milletti, Loriano Storchi, Gianluca Sforna, Simon Cross, Gabriele Cruciani:
  Tautomer Enumeration and Stability Prediction for Virtual Screening on Large Chemical Databases. 68-75

Computational Biochemistry

• 
  Shailesh Sharma, Antonio Rosato:
  Role of the N-Terminal Tail of Metal-Transporting P_1B-type ATPases from Genome-Wide Analysis and Molecular Dynamics Simulations. 76-83
• 
  Oliver Korb, Thomas Stützle, Thomas E. Exner:
  Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS. 84-96

Pharmaceutical Modeling

• 
  Habibah A. Wahab, Yee-Siew Choong, Pazilah Ibrahim, Amirin Sadikun, Thomas Scior:
  Elucidating Isoniazid Resistance Using Molecular Modeling. 97-107
• 
  Andreas Bender, Jeremy L. Jenkins, Josef Scheiber, Sai Chetan K. Sukuru, Meir Glick, John W. Davies:
  How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space. 108-119
• 
  Guo Li, Kendra M. Haney, Glen E. Kellogg, Yan Zhang:
  Comparative Docking Study of Anibamine as the First Natural Product CCR5 Antagonist in CCR5 Homology Models. 120-132

Bioinformatics

• 
  Alexandre Varnek, Cédric Gaudin, Gilles Marcou, Igor I. Baskin, Anil Kumar Pandey, Igor V. Tetko:
  Inductive Transfer of Knowledge: Application of Multi-Task Learning and Feature Net Approaches to Model Tissue-Air Partition Coefficients. 133-144

Software Description

• 
  Ting Zhou, Amedeo Caflisch:
  Data Management System for Distributed Virtual Screening. 145-152

Book Reviews

• 
  Thomas Engel:
  Book Review of Molecular Design (Concepts and Applications). 153

Volume 49, Number 2, February 2009

Noordwijkerhout 2009
Chemical Information

• 
  Chia-Wei Chu, John D. Holliday, Peter Willett:
  Effect of Data Standardization on Chemical Clustering and Similarity Searching. 155-161
• 
  Eugen Lounkine, Jürgen Bajorath:
  Topological Fragment Index for the Analysis of Molecular Substructures and Their Topological Environment in Active Compounds. 162-168
• 
  Sebastian G. Rohrer, Knut Baumann:
  Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data. 169-184
• 
  Jenny Chen, John D. Holliday, John Bradshaw:
  A Machine Learning Approach to Weighting Schemes in the Data Fusion of Similarity Coefficients. 185-194
• 
  George Papadatos, Anthony W. J. Cooper, Visakan Kadirkamanathan, Simon J. F. Macdonald, Iain M. McLay, Stephen D. Pickett, John Pritchard, Peter Willett, Valerie J. Gillet:
  Analysis of Neighborhood Behavior in Lead Optimization and Array Design. 195-208
• 
  Modest von Korff, Joël Freyss, Thomas Sander:
  Comparison of Ligand- and Structure-Based Virtual Screening on the DUD Data Set. 209-231
• 
  Thomas Sander, Joël Freyss, Modest von Korff, Jacqueline Renée Reich, Christian Rufener:
  OSIRIS, an Entirely in-House Developed Drug Discovery Informatics System. 232-246
• 
  Britta Nisius, Andreas H. Göller:
  Similarity-Based Classifier Using Topomers to Provide a Knowledge Base for hERG Channel Inhibition. 247-256
• 
  Andrew Smellie:
  Compressed Binary Bit Trees: A New Data Structure For Accelerating Database Searching. 257-262
• 
  Dazhi Jiao, David J. Wild:
  Extraction of CYP Chemical Interactions from Biomedical Literature Using Natural Language Processing Methods. 263-269

Computational Chemistry

• 
  Uta F. Lessel, Bernd Wellenzohn, Markus Lilienthal, Holger Claussen:
  Searching Fragment Spaces with Feature Trees. 270-279
• 
  Fabrice Moriaud, Olivia Doppelt-Azeroual, Laetitia Martin, Ksenia Oguievetskaia, Kerstin Koch, Artem Vorotyntsev, Stewart A. Adcock, François Delfaud:
  Computational Fragment-Based Approach at PDB Scale by Protein Local Similarity. 280-294

Pharmaceutical Modeling

• 
  Christos A. Nicolaou, Joannis Apostolakis, Constantinos S. Pattichis:
  De Novo Drug Design Using Multiobjective Evolutionary Graphs. 295-307
• 
  Josef Scheiber, Bin Chen, Mariusz Milik, Sai Chetan K. Sukuru, Andreas Bender, Dmitri Mikhailov, Steven Whitebread, Jacques Hamon, Kamal Azzaoui, Laszlo Urban, Meir Glick, John W. Davies, Jeremy L. Jenkins:
  Gaining Insight into Off-Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis. 308-317

Bioinformatics

• 
  Sarah L. Kinnings, Richard M. Jackson:
  Binding Site Similarity Analysis for the Functional Classification of the Protein Kinase Family. 318-329

Chemical Information

• 
  Jamel Meslamani, François André, Michel Petitjean:
  Assessing the Geometric Diversity of Cytochrome P450 Ligand Conformers by Hierarchical Clustering with a Stop Criterion. 330-337
• 
  Andreas Steffen, Thierry Kogej, Christian Tyrchan, Ola Engkvist:
  Comparison of Molecular Fingerprint Methods on the Basis of Biological Profile Data. 338-347
• 
  Eelke van der Horst, Yasushi Okuno, Andreas Bender, Adriaan P. IJzerman:
  Substructure Mining of GPCR Ligands Reveals Activity-Class Specific Functional Groups in an Unbiased Manner. 348-360
• 
  Chern Chuang, Yuan-Chia Fan, Bih-Yaw Jin:
  Generalized Classification Scheme of Toroidal and Helical Carbon Nanotubes. 361-368
• 
  Arkadiusz Ciesielski, Tadeusz M. Krygowski, Michal Cyranski, Michal A. Dobrowolski, Alexandru T. Balaban:
  Are Thermodynamic and Kinetic Stabilities Correlated? A Topological Index of Reactivity toward Electrophiles Used as a Criterion of Aromaticity of Polycyclic Benzenoid Hydrocarbons. 369-376

Computational Chemistry

• 
  Thomas A. Halgren:
  Identifying and Characterizing Binding Sites and Assessing Druggability. 377-389
• 
  Piotr Setny, Joanna Trylska:
  Search for Novel Aminoglycosides by Combining Fragment-Based Virtual Screening and 3D-QSAR Scoring. 390-400

Computational Biochemistry

• 
  Matteo Mozzicafreddo, Massimiliano Cuccioloni, Valentina Cecarini, Anna Maria Eleuteri, Mauro Angeletti:
  Homology Modeling and Docking Analysis of the Interaction between Polyphenols and Mammalian 20S Proteasomes. 401-409
• 
  Janos Nadas, Chenglong Li, Peng George Wang:
  Computational Structure Activity Relationship Studies on the CD1d/Glycolipid/TCR Complex Using AMBER and AUTODOCK. 410-423
• 
  Holly Freedman, J. Torin Huzil, Tyler Luchko, Richard F. Luduena, Jack A. Tuszynski:
  Identification and Characterization of an Intermediate Taxol Binding Site Within Microtubule Nanopores and a Mechanism for Tubulin Isotype Binding Selectivity. 424-436
• 
  Min-Sun Park, Axel L. Dessal, Alan V. Smrcka, Harry A. Stern:
  Evaluating Docking Methods for Prediction of Binding Affinities of Small Molecules to the G Protein βγ Subunits. 437-443

Pharmaceutical Modeling

• 
  Kirk E. Hevener, Wei Zhao, David M. Ball, Kerim Babaoglu, Jianjun Qi, Stephen W. White, Richard E. Lee:
  Validation of Molecular Docking Programs for Virtual Screening against Dihydropteroate Synthase. 444-460
• 
  Hao Tang, Xiang S. Wang, Xi-Ping Huang, Bryan L. Roth, Kyle V. Butler, Alan P. Kozikowski, Mira Jung, Alexander Tropsha:
  Novel Inhibitors of Human Histone Deacetylase (HDAC) Identified by QSAR Modeling of Known Inhibitors, Virtual Screening, and Experimental Validation. 461-476
• 
  José L. Medina-Franco, Karina Martínez-Mayorga, Andreas Bender, Ray M. Marín, Marc A. Giulianotti, Clemencia Pinilla, Richard A. Houghten:
  Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs. 477-491

Software Description

• 
  Mikko J. Vainio, J. Santeri Puranen, Mark S. Johnson:
  ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential. 492-502
• 
  Vladimir V. Diky, Robert D. Chirico, Andrei F. Kazakov, Chris Muzny, Michael Frenkel:
  ThermoData Engine (TDE): Software Implementation of the Dynamic Data Evaluation Concept. 3. Binary Mixtures. 503-517

Volume 49, Number 3, March 2009

Chemical Information

• 
  Roger A. Sayle:
  Foreign Language Translation of Chemical Nomenclature by Computer. 519-530
• 
  Mark Johnson, Veer Shanmugasundaram, Gordon Bundy, Darryl Chapman, Robert Kilkuskie:
  Chemotypic Coverage: A New Basis for Constructing Screening Sublibraries. 531-542
• 
  Cornel Catana:
  Simple Idea to Generate Fragment and Pharmacophore Descriptors and Their Implications in Chemical Informatics. 543-548
• 
  Nikolas Fechner, Andreas Jahn, Georg Hinselmann, Andreas Zell:
  Atomic Local Neighborhood Flexibility Incorporation into a Structured Similarity Measure for QSAR. 549-560
• 
  Eugen Lounkine, Ye Hu, José Batista, Jürgen Bajorath:
  Relevance of Feature Combinations for Similarity Searching Using General or Activity Class-Directed Molecular Fingerprints. 561-570
• 
  Junmei Wang, Tingjun Hou, Xiaojie Xu:
  Aqueous Solubility Prediction Based on Weighted Atom Type Counts and Solvent Accessible Surface Areas. 571-581
• 
  Anne Mai Wassermann, Hanna Geppert, Jürgen Bajorath:
  Searching for Target-Selective Compounds Using Different Combinations of Multiclass Support Vector Machine Ranking Methods, Kernel Functions, and Fingerprint Descriptors. 582-592

Computational Chemistry

• 
  James Law, Zsolt Zsoldos, Anikó Simon, Darryl Reid, Yang Liu, Sing Yoong Khew, A. Peter Johnson, Sarah Major, Robert A. Wade, Howard Y. Ando:
  Route Designer: A Retrosynthetic Analysis Tool Utilizing Automated Retrosynthetic Rule Generation. 593-602
• 
  Hongming Chen, Ulf Borjesson, Ola Engkvist, Thierry Kogej, Mats Svensson, Niklas Blomberg, Dirk Weigelt, Jeremy N. Burrows, Tim Lange:
  ProSAR: A New Methodology for Combinatorial Library Design. 603-614
• 
  Takahiro Kosugi, Isao Nakanishi, Kazuo Kitaura:
  Binding Free Energy Calculations of Adenosine Deaminase Inhibitor and the Effect of Methyl Substitution in Inhibitors. 615-622
• 
  Shay Bar-Haim, Ayelet Aharon, Tal Ben-Moshe, Yael Marantz, Hanoch Senderowitz:
  SeleX-CS: A New Consensus Scoring Algorithm for Hit Discovery and Lead Optimization. 623-633
• 
  Polina V. Oliferenko, Alexander A. Oliferenko, Gennadiy Poda, Vladimir A. Palyulin, Nikolai S. Zefirov, Alan R. Katritzky:
  New Developments in Hydrogen Bonding Acidity and Basicity of Small Organic Molecules for the Prediction of Physical and ADMET Properties. Part 2. The Universal Solvation Equation. 634-646
• 
  R. S. K. Vijayan, Prabu Manoharan, Nahren Manuel Mascarenhas, Nanda Ghoshal:
  Hybrid Structure-Based Virtual Screening Protocol for the Identification of Novel BACE1 Inhibitors. 647-657
• 
  Rikke Bergmann, Tommy Liljefors, Morten Dahl Sørensen, Ismael Zamora:
  SHOP: Receptor-Based Scaffold HOPping by GRID-Based Similarity Searches. 658-669
• 
  Matthew Paul Gleeson, Duangkamol Gleeson:
  QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena? 670-677
• 
  Johannes Kirchmair, Simona Distinto, Patrick Markt, Daniela Schuster, Gudrun M. Spitzer, Klaus R. Liedl, Gerhard Wolber:
  How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information. 678-692

Computational Biochemistry

• 
  Tatsuya Yoshikawa, Koki Tsukamoto, Yuichiro Hourai, Kazuhiko Fukui:
  Improving the Accuracy of an Affinity Prediction Method by Using Statistics on Shape Complementarity between Proteins. 693-703

Pharmaceutical Modeling

• 
  Ruchi R. Mittal, Lisa Harris, Ross A. McKinnon, Michael J. Sorich:
  Partial Charge Calculation Method Affects CoMFA QSAR Prediction Accuracy. 704-709
• 
  Frank R. Burden, Mitchell J. Polley, David A. Winkler:
  Toward Novel Universal Descriptors: Charge Fingerprints. 710-715
• 
  Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan:
  Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes. 716-725
• 
  Constantinos Potamitis, Maria Zervou, Vassilis Katsiaras, Panagiotis Zoumpoulakis, Serdar Durdagi, Manthos G. Papadopoulos, Joseph M. Hayes, Simona Golic Grdadolnik, Ioanna Kyrikou, Dimitris Argyropoulos, Georgia Vatougia, Thomas M. Mavromoustakos:
  Antihypertensive Drug Valsartan in Solution and at the AT₁ Receptor: Conformational Analysis, Dynamic NMR Spectroscopy, in Silico Docking, and Molecular Dynamics Simulations. 726-739

Software Description

• 
  Igor V. Filippov, Marc C. Nicklaus:
  Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution. 740-743

Volume 49, Number 4, April 2009

Chemical Information

• 
  Ning Yu, Gregory A. Bakken:
  Efficient Exploration of Large Combinatorial Chemistry Spaces by Monomer-Based Similarity Searching. 745-755
• 
  S. Joshua Swamidass, Chloé-Agathe Azencott, Ting-Wan Lin, Hugo Gramajo, Shiou-Chuan Tsai, Pierre Baldi:
  Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method. 756-766
• 
  Hanna Geppert, Jens Humrich, Dagmar Stumpfe, Thomas Gärtner, Jürgen Bajorath:
  Ligand Prediction from Protein Sequence and Small Molecule Information Using Support Vector Machines and Fingerprint Descriptors. 767-779
• 
  Aniko T. Valko, A. Peter Johnson:
  CLiDE Pro: The Latest Generation of CLiDE, a Tool for Optical Chemical Structure Recognition. 780-787
• 
  Daniel R. Albaugh, L. Mark Hall, Dennis W. Hill, Tzipporah M. Kertesz, Marc Parham, Lowell H. Hall, David F. Grant:
  Prediction of HPLC Retention Index Using Artificial Neural Networks and IGroup E-State Indices. 788-799
• 
  Jochen Schlosser, Matthias Rarey:
  Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds. 800-809
• 
  Violeta I. Pérez-Nueno, Sofia Pettersson, David W. Ritchie, José I. Borrell, Jordi Teixidó:
  Discovery of Novel HIV Entry Inhibitors for the CXCR4 Receptor by Prospective Virtual Screening. 810-823
• 
  Mohammad Goodarzi, Matheus P. Freitas, Richard Jensen:
  Feature Selection and Linear/Nonlinear Regression Methods for the Accurate Prediction of Glycogen Synthase Kinase-3β Inhibitory Activities. 824-832

Computational Chemistry

• 
  Jernej Stare, Neil J. Henson, Juergen Eckert:
  Mechanistic Aspects of Propene Epoxidation by Hydrogen Peroxide. Catalytic Role of Water Molecules, External Electric Field, and Zeolite Framework of TS-1. 833-846
• 
  Chittima Laohpongspaisan, Thanyada Rungrotmongkol, Pathumwadee Intharathep, Maturos Malaisree, Panita Decha, Ornjira Aruksakunwong, Pornthep Sompornpisut, Supot Hannongbua:
  Why Amantadine Loses Its Function in Influenza M2 Mutants: MD Simulations. 847-852
• 
  Kazuya Yasuo, Noriyuki Yamaotsu, Hiroaki Gouda, Hideki Tsujishita, Shuichi Hirono:
  Structure-Based CoMFA As a Predictive Model - CYP2C9 Inhibitors As a Test Case. 853-864
• 
  Ori Kalid, Nir Ben-Tal:
  Study of MDM2 Binding to p53-Analogues: Affinity, Helicity, and Applicability to Drug Design. 865-876
• 
  Chin Yee Liew, Xiao Hua Ma, Xianghui Liu, Chun Wei Yap:
  SVM Model for Virtual Screening of Lck Inhibitors. 877-885
• 
  Jans H. Alzate-Morales, Julio Caballero, Ariela Vergara Jaque, Fernando D. González Nilo:
  Insights into the Structural Basis of N2 and O6 Substituted Guanine Derivatives as Cyclin-Dependent Kinase 2 (CDK2) Inhibitors: Prediction of the Binding Modes and Potency of the inhibitors by Docking and ONIOM Calculations. 886-899
• 
  Antonio Macchiarulo, Roberto Nuti, Gokcen Eren, Roberto Pellicciari:
  Charting the Chemical Space of Target Sites: Insights into the Binding Modes of Amine and Amidine Groups. 900-912
• 
  Pedro Fong, Jonathan P. McNamara, Ian H. Hillier, Richard A. Bryce:
  Assessment of QM/MM Scoring Functions for Molecular Docking to HIV-1 Protease. 913-924
• 
  Yoshifumi Fukunishi, Tadaaki Mashimo, Masaya Orita, Kazuki Ohno, Haruki Nakamura:
  In Silico Fragment Screening by Replica Generation (FSRG) Method for Fragment-Based Drug Design. 925-933
• 
  Matthew Clark, Siavash Meshkat, Jeffrey S. Wiseman:
  Grand Canonical Free-Energy Calculations of Protein-Ligand Binding. 934-943
• 
  Robert S. Paton, Jonathan M. Goodman:
  Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions. 944-955
• 
  Johannes Schwöbel, Ralf-Uwe Ebert, Ralph Kühne, Gerrit Schüürmann:
  Prediction of the Intrinsic Hydrogen Bond Acceptor Strength of Organic Compounds by Local Molecular Parameters. 956-962

Computational Biochemistry

• 
  Marius Retegan, Anne Milet, Hélene Jamet:
  Exploring the Binding of Inhibitors Derived from Tetrabromobenzimidazole to the CK2 Protein Using a QM/MM-PB/SA Approach. 963-971
• 
  Francesco Pietra:
  Docking and MD Simulations of the Interaction of the Tarantula Peptide Psalmotoxin-1 with ASIC1a Channels Using a Homology Model. 972-977

Pharmaceutical Modeling

• 
  Areej M. Abu Hammad, Mutasem O. Taha:
  Pharmacophore Modeling, Quantitative Structure-Activity Relationship Analysis, and Shape-Complemented in Silico Screening Allow Access to Novel Influenza Neuraminidase Inhibitors. 978-996
• 
  Christopher R. Corbeil, Nicolas Moitessier:
  Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs. 997-1009
• 
  Narender Singh, Rajarshi Guha, Marc A. Giulianotti, Clemencia Pinilla, Richard A. Houghten, José L. Medina-Franco:
  Chemoinformatic Analysis of Combinatorial Libraries, Drugs, Natural Products, and Molecular Libraries Small Molecule Repository. 1010-1024
• 
  Timothy J. Ritchie, Christopher N. Luscombe, Simon J. F. Macdonald:
  Analysis of the Calculated Physicochemical Properties of Respiratory Drugs: Can We Design for Inhaled Drugs Yet? 1025-1032
• 
  Xing-long Zhang, Xun Li, Renxiao Wang:
  Interpretation of the Binding Affinities of PTP1B Inhibitors with the MM-GB/SA Method and the X-Score Scoring Function. 1033-1048
• 
  Nathanael Weill, Didier Rognan:
  Development and Validation of a Novel Protein-Ligand Fingerprint To Mine Chemogenomic Space: Application to G Protein-Coupled Receptors and Their Ligands. 1049-1062
• 
  Gudrun M. Spitzer, Bernd Wellenzohn, Patrick Markt, Johannes Kirchmair, Thierry Langer, Klaus R. Liedl:
  Hydrogen-Bonding Patterns of Minor Groove-Binder-DNA Complexes Reveal Criteria for Discovery of New Scaffolds. 1063-1069
• 
  Carolina Horta Andrade, Kerly F. M. Pasqualoto, Elizabeth I. Ferreira, Anton J. Hopfinger:
  Rational Design and 3D-Pharmacophore Mapping of 5′-Thiourea-Substituted α-Thymidine Analogues as Mycobacterial TMPK Inhibitors. 1070-1078
• 
  Tiejun Cheng, Xun Li, Yan Li, Zhihai Liu, Renxiao Wang:
  Comparative Assessment of Scoring Functions on a Diverse Test Set. 1079-1093
• 
  Agnieszka A. Kaczor, Urszula A. Kijkowska-Murak, Christiane Kronbach, Klaus Unverferth, Dariusz Matosiuk:
  Modeling of Glutamate GluR6 Receptor and Its Interactions with Novel Noncompetitive Antagonists. 1094-1104
• 
  David Hecht, Gary B. Fogel:
  A Novel In Silico Approach to Drug Discovery via Computational Intelligence. 1105-1121

Bioinformatics

• 
  Daichi Shigemizu, Michihiro Araki, Shujiro Okuda, Susumu Goto, Minoru Kanehisa:
  Extraction and Analysis of Chemical Modification Patterns in Drug Development. 1122-1129
• 
  M. Michael Gromiha:
  Multiple Contact Network Is a Key Determinant to Protein Folding Rates. 1130-1135

Computer Software Reviews

• 
  Tim Claridge:
  Software Review of MNova: NMR Data Processing, Analysis, and Prediction Software. 1136-1137

Volume 49, Number 5, May 2009

Letter

• 
  Serdar Durdagi, Claudiu T. Supuran, T. Amanda Strom, Nadjmeh Doostdar, Mananjali K. Kumar, Andrew R. Barron, Thomas M. Mavromoustakos, Manthos G. Papadopoulos:
  In Silico Drug Screening Approach for the Design of Magic Bullets: A Successful Example with Anti-HIV Fullerene Derivatized Amino Acids. 1139-1143

Chemical Information

• 
  Yan-Ping Zhou, Li-Juan Tang, Jian Jiao, Dandan Song, Jian-Hui Jiang, Ru-Qin Yu:
  Modified Particle Swarm Optimization Algorithm for Adaptively Configuring Globally Optimal Classification and Regression Trees. 1144-1153
• 
  Mark D. Mackey, James L. Melville:
  Better than Random? The Chemotype Enrichment Problem. 1154-1162
• 
  Hina Patel, Michael J. Bodkin, Beining Chen, Valerie J. Gillet:
  Knowledge-Based Approach to de Novo Design Using Reaction Vectors. 1163-1184
• 
  Ravi Nandigam, Sangtae Kim, Juswinder Singh, Claudio Chuaqui:
  Position Specific Interaction Dependent Scoring Technique for Virtual Screening Based on Weighted Protein-Ligand Interaction Fingerprint Profiles. 1185-1192
• 
  Aysha Al Khalifa, Maciej Haranczyk, John D. Holliday:
  Comparison of Nonbinary Similarity Coefficients for Similarity Searching, Clustering and Compound Selection. 1193-1201

Computational Chemistry

• 
  Maris Lapins, Jarl E. S. Wikberg:
  Proteochemometric Modeling of Drug Resistance over the Mutational Space for Multiple HIV Protease Variants and Multiple Protease Inhibitors. 1202-1210
• 
  Britta Nisius, Ulrich Rester:
  Fragment Shuffling: An Automated Workflow for Three-Dimensional Fragment-Based Ligand Design. 1211-1222
• 
  Sergio Giuffrida, Giampaolo Barone, Dario Duca:
  Adsorbed CO on Group 10 Metal Fragments: A DFT Study. 1223-1233
• 
  Peter W. Kenny:
  Hydrogen Bonding, Electrostatic Potential, and Molecular Design. 1234-1244
• 
  Violeta I. Pérez-Nueno, Obdulia Rabal, José I. Borrell, Jordi Teixidó:
  APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening. 1245-1260

Computational Biochemistry

• 
  Germán Moltó, María Suárez, Pablo Tortosa, José M. Alonso, Vicente Hernández, Alfonso Jaramillo:
  Protein Design Based on Parallel Dimensional Reduction. 1261-1271

Pharmaceutical Modeling

• 
  Sara E. Nichols, Robert A. Domaoal, Vinay V. Thakur, Julian Tirado-Rives, Karen S. Anderson, William L. Jorgensen:
  Discovery of Wild-Type and Y181C Mutant Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors Using Virtual Screening with Multiple Protein Structures. 1272-1279
• 
  Markus Krier, Michael C. Hutter:
  Bioisosteric Similarity of Molecules Based on Structural Alignment and Observed Chemical Replacements in Drugs. 1280-1297
• 
  Vishal Prakash Zambre, Prashant Revan Murumkar, Rajani Giridhar, Mange Ram Yadav:
  Structural Investigations of Acridine Derivatives by CoMFA and CoMSIA Reveal Novel Insight into Their Structures toward DNA G-Quadruplex Mediated Telomerase Inhibition and Offer a Highly Predictive 3D-Model for Substituted Acridines. 1298-1311

Volume 49, Number 6, June 2009

Chemical Information

• 
  Jerry Osagie Ebalunode, Weifan Zheng:
  Unconventional 2D Shape Similarity Method Affords Comparable Enrichment as a 3D Shape Method in Virtual Screening Experiments. 1313-1320
• 
  Grazyna Nowak, Grzegorz Fic:
  Machine Learning Approach to Discovering Cascade Reaction Patterns. Application to Reaction Pathways Prediction. 1321-1329
• 
  Kristian Birchall, Valerie J. Gillet, Peter Willett, Pierre Ducrot, Claude Luttmann:
  Use of Reduced Graphs To Encode Bioisosterism for Similarity-Based Virtual Screening. 1330-1346
• 
  Britta Nisius, Martin Vogt, Jürgen Bajorath:
  Development of a Fingerprint Reduction Approach for Bayesian Similarity Searching Based on Kullback-Leibler Divergence Analysis. 1347-1358
• 
  Eugen Lounkine, Dagmar Stumpfe, Jürgen Bajorath:
  Molecular Formal Concept Analysis for Compound Selectivity Profiling in Biologically Annotated Databases. 1359-1368
• 
  Yuan Wang, Jürgen Bajorath:
  Development of a Compound Class-Directed Similarity Coefficient That Accounts for Molecular Complexity Effects in Fingerprint Searching. 1369-1376

Computational Chemistry

• 
  Terufumi Takagi, Michiko Amano, Masaki Tomimoto:
  Novel Method for the Evaluation of 3D Conformation Generators. 1377-1388
• 
  Vladimir Potemkin, Alexander A. Pogrebnoy, Maria A. Grishina:
  Technique for Energy Decomposition in the Study of "Receptor-Ligand" Complexes. 1389-1406
• 
  Pablo D. Dans, Elena Laura Coitiño:
  Density Functional Theory Characterization and Descriptive Analysis of Cisplatin and Related Compounds. 1407-1419
• 
  Zhao Wang, Yan Lu, William Seibel, Duane D. Miller, Wei Li:
  Identifying Novel Molecular Structures for Advanced Melanoma by Ligand-Based Virtual Screening. 1420-1427
• 
  João Paulo Ataide Martins, Euzébio G. Barbosa, Kerly F. M. Pasqualoto, Márcia M. C. Ferreira:
  LQTA-QSAR: A New 4D-QSAR Methodology. 1428-1436
• 
  Matthew Paul Gleeson, Duangkamol Gleeson:
  QM/MM As a Tool in Fragment Based Drug Discovery. A Cross-Docking, Rescoring Study of Kinase Inhibitors. 1437-1448
• 
  John Manchester, Ryszard Czerminski:
  CAUTION: Popular "Benchmark" Data Sets Do Not Distinguish the Merits of 3D QSAR Methods. 1449-1454
• 
  Jason B. Cross, David C. Thompson, Brajesh K. Rai, J. Christian Baber, Kristi Yi Fan, Yongbo Hu, Christine Humblet:
  Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy. 1455-1474
• 
  Mohammad Goodarzi, Pablo Duchowicz, Chih-Hung Wu, Francisco M. Fernández, Eduardo A. Castro:
  New Hybrid Genetic Based Support Vector Regression as QSAR Approach for Analyzing Flavonoids-GABA(A) Complexes. 1475-1485
• 
  Katja Hansen, Fabian Rathke, Timon Schroeter, Georg Rast, Thomas Fox, Jan M. Kriegl, Sebastian Mika:
  Bias-Correction of Regression Models: A Case Study on hERG Inhibition. 1486-1496
• 
  Michael Devereux, Paul L. A. Popelier, Iain M. McLay:
  Quantum Isostere Database: A Web-Based Tool Using Quantum Chemical Topology To Predict Bioisosteric Replacements for Drug Design. 1497-1513
• 
  Stefan Senger:
  Using Tversky Similarity Searches for Core Hopping: Finding the Needles in the Haystack. 1514-1524

Computational Biochemistry

• 
  Oliver Sacher, Martin Reitz, Johann Gasteiger:
  Investigations of Enzyme-Catalyzed Reactions Based on Physicochemical Descriptors Applied to Hydrolases. 1525-1534
• 
  Tim ten Brink, Thomas E. Exner:
  Influence of Protonation, Tautomeric, and Stereoisomeric States on Protein-Ligand Docking Results. 1535-1546
• 
  Nicos Angelopoulos, Andreas Hadjiprocopis, Malcolm D. Walkinshaw:
  Bayesian Model Averaging for Ligand Discovery. 1547-1557

Pharmaceutical Modeling

• 
  Wai Keat Yam, Habibah A. Wahab:
  Molecular Insights into 14-Membered Macrolides Using the MM-PBSA Method. 1558-1567
• 
  Pablo Englebienne, Nicolas Moitessier:
  Docking Ligands into Flexible and Solvated Macromolecules. 4. Are Popular Scoring Functions Accurate for this Class of Proteins? 1568-1580
• 
  Rohit Tiwari, Kiran Mahasenan, Ryan E. Pavlovicz, Chenglong Li, Werner Tjarks:
  Carborane Clusters in Computational Drug Design: A Comparative Docking Evaluation Using AutoDock, FlexX, Glide, and Surflex. 1581-1589
• 
  Shailendra S. Chaudhaery, Kuldeep K. Roy, Anil K. Saxena:
  Consensus Superiority of the Pharmacophore-Based Alignment, Over Maximum Common Substructure (MCS): 3D-QSAR Studies on Carbamates as Acetylcholinesterase Inhibitors. 1590-1601
• 
  Agostino Bruno, Antonio Entrena Guadix, Gabriele Costantino:
  Molecular Dynamics Simulation of the Heterodimeric mGluR2/5HT_2A Complex. An Atomistic Resolution Study of a Potential New Target in Psychiatric Conditions. 1602-1616
• 
  J. Willem M. Nissink:
  Simple Size-Independent Measure of Ligand Efficiency. 1617-1622

Volume 49, Number 7, July 2009

Perspective

• 
  David Zanuy, Gema Ballano, Ana I. Jiménez, Jordi Casanovas, Nurit Haspel, Carlos Cativiela, David Curcó, Ruth Nussinov, Carlos Alemán:
  Protein Segments with Conformationally Restricted Amino Acids Can Control Supramolecular Organization at the Nanoscale. 1623-1629

Chemical Information

• 
  Peter S. Kutchukian, David Lou, Eugene I. Shakhnovich:
  FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules Occupying Druglike Chemical Space. 1630-1642
• 
  Doo Nam Kim, Kwang-Hwi Cho, Wonseok Oh, Chang-Joon Lee, Sungkwang Lee, Jihoon Jung, Kyoung Tai No:
  E_aMEAD: Activation Energy Prediction of Cytochrome P450 Mediated Metabolism with Effective Atomic Descriptors. 1643-1654
• 
  Matthias Dehmer, Kurt Varmuza, Stephan Borgert, Frank Emmert-Streib:
  On Entropy-Based Molecular Descriptors: Statistical Analysis of Real and Synthetic Chemical Structures. 1655-1663
• 
  Chern Chuang, Bih-Yaw Jin:
  Systematics of High-Genus Fullerenes. 1664-1668
• 
  Viviana Consonni, Davide Ballabio, Roberto Todeschini:
  Comments on the Definition of the Q² Parameter for QSAR Validation. 1669-1678
• 
  Chern Chuang, Yuan-Chia Fan, Bih-Yaw Jin:
  Dual Space Approach to the Classification of Toroidal Carbon Nanotubes. 1679-1686
• 
  Yuan Wang, Hanna Geppert, Jürgen Bajorath:
  Shannon Entropy-Based Fingerprint Similarity Search Strategy. 1687-1691

Computational Chemistry

• 
  Arthur N. Mayeno, Jonathan L. Robinson, Raymond S. H. Yang, Brad Reisfeld:
  Predicting Activation Enthalpies of Cytochrome-P450-Mediated Hydrogen Abstractions. 2. Comparison of Semiempirical PM3, SAM1, and AM1 with a Density Functional Theory Method. 1692-1703
• 
  Miklos Feher, Christopher I. Williams:
  Effect of Input Differences on the Results of Docking Calculations. 1704-1714
• 
  Tiziano Tuccinardi, Gabriella Ortore, M. Amélia Santos, Sérgio M. Marques, Elisa Nuti, Armando Rossello, Adriano Martinelli:
  Multitemplate Alignment Method for the Development of a Reliable 3D-QSAR Model for the Analysis of MMP3 Inhibitors. 1715-1724

Computational Biochemistry

• 
  Bo Li, Zhenming Liu, Liang Ren Zhang, Li He Zhang:
  Multiple-Docking and Affinity Fingerprint Methods for Protein Classification and Inhibitors Selection. 1725-1733
• 
  Indu R. Chandrashekaran, Gita Subba Rao, Sudha M. Cowsik:
  Molecular Modeling of the Peptide Agonist-Binding Site in a Neurokinin-2 Receptor. 1734-1740
• 
  Sohini Basu, Srikanta Sen:
  Turning a Mesophilic Protein into a Thermophilic One: A Computational Approach Based on 3D Structural Features. 1741-1750

Pharmaceutical Modeling

• 
  Stefano Alcaro, Anna Artese, Francesca Ceccherini-Silberstein, Francesco Ortuso, Carlo-Federico Perno, Tobias Sing, Valentina Svicher:
  Molecular Dynamics and Free Energy Studies on the Wild-Type and Mutated HIV-1 Protease Complexed with Four Approved Drugs: Mechanism of Binding and Drug Resistance. 1751-1761
• 
  Dragos Horvath, Gilles Marcou, Alexandre Varnek:
  Predicting the Predictability: A Unified Approach to the Applicability Domain Problem of QSAR Models. 1762-1776
• 
  Ira Musmuca, Silvia Simeoni, Antonia Caroli, Rino Ragno:
  Small-Molecule Interferon Inducers. Toward the Comprehension of the Molecular Determinants through Ligand-Based Approaches. 1777-1786
• 
  Sivaprakasam Prasanna, Perrer N. Tosso, Robert J. Doerksen:
  Structure-Activity Relationship and Comparative Docking Studies for Cycloguanil Analogs as PfDHFR-TS Inhibitors. 1787-1796
• 
  Bradley C. Pearce, David R. Langley, Jia Kang, Hongwei Huang, Amit Kulkarni:
  E-Novo: An Automated Workflow for Efficient Structure-Based Lead Optimization. 1797-1809
• 
  Ruchi R. Mittal, Ross A. McKinnon, Michael J. Sorich:
  Comparison Data Sets for Benchmarking QSAR Methodologies in Lead Optimization. 1810-1820

Bioinformatics

• 
  Andrzej Galat:
  On Transversal Hydrophobicity of Some Proteins and Their Modules. 1821-1830
• 
  Su Qiu, Hong Yi, Hui Liu, Zhijian Cao, Yingliang Wu, Wenxin Li:
  Molecular Information of Charybdotoxin Blockade in the Large Conductance Calcium-activated Potassium Channel. 1831-1838
• 
  Diogo A. R. S. Latino, João Aires-de-Sousa:
  Assignment of EC Numbers to Enzymatic Reactions with MOLMAP Reaction Descriptors and Random Forests. 1839-1846

Software Description

• 
  Gareth Jones, Yinghong Gao, Carleton R. Sage:
  Elucidating Molecular Overlays from Pairwise Alignments Using a Genetic Algorithm. 1847-1855

Volume 49, Number 8, August 2009

Chemical Information

• 
  Qianyi Zhang, Jacqueline M. Hughes-Oliver, Raymond T. Ng:
  A Model-Based Ensembling Approach for Developing QSARs. 1857-1865
• 
  Pierre Baldi, Daniel S. Hirschberg:
  An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases. 1866-1870
• 
  Noel M. O'Boyle, John W. Liebeschuetz, Jason C. Cole:
  Testing Assumptions and Hypotheses for Rescoring Success in Protein-Ligand Docking. 1871-1878

Computational Chemistry

• 
  Whanchul Shin, Seung Ah Hyun, Chong Hak Chae, Jae Kyung Chon:
  Flexible Alignment of Small Molecules Using the Penalty Method. 1879-1888
• 
  J. Christian Baber, David C. Thompson, Jason B. Cross, Christine Humblet:
  GARD: A Generally Applicable Replacement for RMSD. 1889-1900
• 
  Matthew Clark, Siavash Meshkat, George T. Talbot, Paolo Carnevali, Jeffrey S. Wiseman:
  Fragment-Based Computation of Binding Free Energies by Systematic Sampling. 1901-1913
• 
  Alex P. Harding, David C. Wedge, Paul L. A. Popelier:
  pK_a Prediction from "Quantum Chemical Topology" Descriptors. 1914-1924

Computational Biochemistry

• 
  Clarisse G. Ricci, Paulo A. Netz:
  Docking Studies on DNA-Ligand Interactions: Building and Application of a Protocol To Identify the Binding Mode. 1925-1935
• 
  Xiao-Lei Zhu, Ge-Fei Hao, Chang-Guo Zhan, Guangfu Yang:
  Computational Simulations of the Interactions between Acetyl-Coenzyme-A Carboxylase and Clodinafop: Resistance Mechanism Due to Active and Nonactive Site Mutations. 1936-1943
• 
  Yoshifumi Fukunishi, Daisuke Mitomo, Haruki Nakamura:
  Protein-Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method. 1944-1951

Pharmaceutical Modeling

• 
  John W. Raymond, Ian A. Watson, Abdelaziz Mahoui:
  Rationalizing Lead Optimization by Associating Quantitative Relevance with Molecular Structure Modification. 1952-1962
• 
  Qi Wang, Robert H. Mach, David E. Reichert:
  Docking and 3D-QSAR Studies on Isatin Sulfonamide Analogues as Caspase-3 Inhibitors. 1963-1973
• 
  Robert P. Sheridan, Kiyean Nam, Vladimir N. Maiorov, Daniel R. McMasters, Wendy D. Cornell:
  QSAR Models for Predicting the Similarity in Binding Profiles for Pairs of Protein Kinases and the Variation of Models between Experimental Data Sets. 1974-1985

Bioinformatics

• 
  Harsha Gurulingappa, Corinna Kolárik, Martin Hofmann-Apitius, Juliane Fluck:
  Concept-Based Semi-Automatic Classification of Drugs. 1986-1992
• 
  Jungkap Park, Gus R. Rosania, Kazuhiro Saitou:
  Tunable Machine Vision-Based Strategy for Automated Annotation of Chemical Databases. 1993-2001
• 
  Li-Juan Tang, Wen Du, Haiyan Fu, Jian-Hui Jiang, Hai-Long Wu, Guo-Li Shen, Ru-Qin Yu:
  New Variable Selection Method Using Interval Segmentation Purity with Application to Blockwise Kernel Transform Support Vector Machine Classification of High-Dimensional Microarray Data. 2002-2009

Computer Software Reviews

• 
  Beth Thomsett-Scott:
  Software Review of Origin 8. 2010

Book Reviews

• 
  Robert E. Buntrock:
  Information and Emotion: The Emergent Affective Paradigm in Information Behavior Research and Theory. 2011
• 
  Robert E. Buntrock:
  Write Like a Chemist. 2011-2012

Volume 49, Number 9, September 2009

Perspective

• 
  Adam C. Lee, Gordon M. Crippen:
  Predicting pK_a. 2013-2033

Chemical Information

• 
  Jonathan H. Chen, Pierre Baldi:
  No Electron Left Behind: A Rule-Based Expert System To Predict Chemical Reactions and Reaction Mechanisms. 2034-2043
• 
  Bin Chen, David J. Wild, Rajarshi Guha:
  PubChem as a Source of Polypharmacology. 2044-2055
• 
  Sarah L. Kinnings, Richard M. Jackson:
  LigMatch: A Multiple Structure-Based Ligand Matching Method for 3D Virtual Screening. 2056-2066

Computational Chemistry

• 
  Monika Nocker, Sandra Handschuh, Christofer S. Tautermann, Klaus R. Liedl:
  Theoretical Prediction of Hydrogen Bond Strength for Use in Molecular Modeling. 2067-2076
• 
  Katja Hansen, Sebastian Mika, Timon Schroeter, Andreas Sutter, Antonius ter Laak, Thomas Steger-Hartmann, Nikolaus Heinrich, Klaus-Robert Müller:
  Benchmark Data Set for in Silico Prediction of Ames Mutagenicity. 2077-2081
• 
  Valérie Campagna-Slater, Matthieu Schapira:
  Evaluation of Virtual Screening as a Tool for Chemical Genetic Applications. 2082-2091
• 
  Meng Lei, Xin Zhao, Zhanli Wang, Yongqiang Zhu:
  Pharmacophore Modeling, Docking Studies, and Synthesis of Novel Dipeptide Proteasome Inhibitors Containing Boron Atoms. 2092-2100

Computational Biochemistry

• 
  X. H. Liu, Xiao Hua Ma, C. Y. Tan, Yu Yang Jiang, M. L. Go, Boon Chuan Low, Yuzong Chen:
  Virtual Screening of Abl Inhibitors from Large Compound Libraries by Support Vector Machines. 2101-2110
• 
  Thomas R. Cundari, Angela K. Wilson, Michael L. Drummond, Hector Emanuel Gonzalez, Kameron R. Jorgensen, Stacy Payne, Jordan Braunfeld, Margarita De Jesus, Vanessa M. Johnson:
  CO₂-Formatics: How Do Proteins Bind Carbon Dioxide? 2111-2115

Pharmaceutical Modeling

• 
  Izhar Wallach, Ryan H. Lilien:
  Predicting Multiple Ligand Binding Modes Using Self-Consistent Pharmacophore Hypotheses. 2116-2128
• 
  Ángel Durán, Ismael Zamora, Manuel Pastor:
  Suitability of GRIND-Based Principal Properties for the Description of Molecular Similarity and Ligand-Based Virtual Screening. 2129-2138

Bioinformatics

• 
  Brian T. Sutch, Eric J. Chambers, Melina Z. Bayramyan, Timothy K. Gallaher, Ian S. Haworth:
  Similarity of Protein-RNA Interfaces Based on Motif Analysis. 2139-2146
• 
  Aysam Guerler, Connie Wang, Ernst-Walter Knapp:
  Symmetric Structures in the Universe of Protein Folds. 2147-2151

Book Reviews

• 
  Robert E. Buntrock:
  The Chicago Guide to Your Career in Science. A Toolkit for Students and Postdocs. 2152
• 
  Stephen R. Heller:
  Book Review of Google: The Digital Gutenberg. 2152-2153

Volume 49, Number 10, October 2009

Chemical Information

• 
  Anne Mai Wassermann, Hanna Geppert, Jürgen Bajorath:
  Ligand Prediction for Orphan Targets Using Support Vector Machines and Various Target-Ligand Kernels Is Dominated by Nearest Neighbor Effects. 2155-2167
• 
  Pekka Tiikkainen, Patrick Markt, Gerhard Wolber, Johannes Kirchmair, Simona Distinto, Antti Poso, Olli-P. Kallioniemi:
  Critical Comparison of Virtual Screening Methods against the MUV Data Set. 2168-2178
• 
  Mihiret Tekeste Sisay, Lisa Peltason, Jürgen Bajorath:
  Structural Interpretation of Activity Cliffs Revealed by Systematic Analysis of Structure-Activity Relationships in Analog Series. 2179-2189
• 
  Nikil Wale, George Karypis:
  Target Fishing for Chemical Compounds Using Target-Ligand Activity Data and Ranking Based Methods. 2190-2201
• 
  Bruce A. Posner, Hualin Xi, James E. J. Mills:
  Enhanced HTS Hit Selection via a Local Hit Rate Analysis. 2202-2210
• 
  Willem P. van Hoorn, Andrew Bell:
  Searching Chemical Space with the Bayesian Idea Generator. 2211-2220
• 
  Jeremy Kolpak, Peter J. Connolly, Victor S. Lobanov, Dimitris K. Agrafiotis:
  Enhanced SAR Maps: Expanding the Data Rendering Capabilities of a Popular Medicinal Chemistry Tool. 2221-2230

Computational Chemistry

• 
  J. Anthony Wilson, Andreas Bender, Taner Kaya, Paul A. Clemons:
  Alpha Shapes Applied to Molecular Shape Characterization Exhibit Novel Properties Compared to Established Shape Descriptors. 2231-2241
• 
  Pascal Bonnet, Dimitris K. Agrafiotis, Fangqiang Zhu, Eric J. Martin:
  Conformational Analysis of Macrocycles: Finding What Common Search Methods Miss. 2242-2259
• 
  Domingo González-Ruiz, Holger Gohlke:
  Steering Protein-Ligand Docking with Quantitative NMR Chemical Shift Perturbations. 2260-2271
• 
  Antonio Macchiarulo, Janet M. Thornton, Irene Nobeli:
  Mapping Human Metabolic Pathways in the Small Molecule Chemical Space. 2272-2289
• 
  Orazio Nicolotti, Ilenia Giangreco, Teresa Fabiola Miscioscia, Angelo Carotti:
  Improving Quantitative Structure-Activity Relationships through Multiobjective Optimization. 2290-2302
• 
  Axel Griewel, Ole Kayser, Jochen Schlosser, Matthias Rarey:
  Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size. 2303-2311
• 
  Poonsiri Thipnate, Jianzhong Liu, Supa Hannongbua, Anton J. Hopfinger:
  3D Pharmacophore Mapping Using 4D QSAR Analysis for the Cytotoxicity of Lamellarins Against Human Hormone-Dependent T47D Breast Cancer Cells. 2312-2322
• 
  Thanyarat Udommaneethanakit, Thanyada Rungrotmongkol, Urban Bren, Vladimir Frecer, Stanislav Miertus:
  Dynamic Behavior of Avian Influenza A Virus Neuraminidase Subtype H5N1 in Complex with Oseltamivir, Zanamivir, Peramivir, and Their Phosphonate Analogues. 2323-2332
• 
  Oranit Dror, Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson:
  Novel Approach for Efficient Pharmacophore-Based Virtual Screening: Method and Applications. 2333-2343

Computational Biochemistry

• 
  Peng Zhou, Jianwei Zou, Feifei Tian, Zhicai Shang:
  Fluorine Bonding - How Does It Work In Protein-Ligand Interactions? 2344-2355

Pharmaceutical Modeling

• 
  Noeris K. Salam, Roberto Nuti, Woody Sherman:
  Novel Method for Generating Structure-Based Pharmacophores Using Energetic Analysis. 2356-2368
• 
  Yen-Tseng Wang, Zhi-Yuan Su, Chang-Huain Hsieh, Cheng-Lung Chen:
  Predictions of Binding for Dopamine D2 Receptor Antagonists by the SIE Method. 2369-2375
• 
  De-Xin Kong, Wei Ren, Wei Lu, Hong-yu Zhang:
  Do Biologically Relevant Compounds Have More Chance To Be Drugs? 2376-2381
• 
  Jae Yoon Chung, Jung-Mi Hah, Art E. Cho:
  Correlation between Performance of QM/MM Docking and Simple Classification of Binding Sites. 2382-2387
• 
  Oliver Koch, Jason C. Cole, Peter Block, Gerhard Klebe:
  Secbase: Database Module To Retrieve Secondary Structure Elements with Ligand Binding Motifs. 2388-2402

Bioinformatics

• 
  Onur Dagliyan, I. Halil Kavakli, Metin Türkay:
  Classification of Cytochrome P450 Inhibitors with Respect to Binding Free Energy and pIC₅₀ Using Common Molecular Descriptors. 2403-2411

Software Description

• 
  Sanjit Roopra, Bernhard Knapp, Ulrich Omasits, Wolfgang Schreiner:
  jSimMacs for GROMACS: A Java Application for Advanced Molecular Dynamics Simulations with Remote Access Capability. 2412-2417

Volume 49, Number 11, November 2009

• 
  Hui Sun Lee, Cheol Soon Lee, Jeong Sook Kim, Dong Hou Kim, Han Choe:
  Improving Virtual Screening Performance against Conformational Variations of Receptors by Shape Matching with Ligand Binding Pocket. 2419-2428
• 
  Zsolt Lepp, Chunfei Huang, Takashi Okada:
  Finding Key Members in Compound Libraries by Analyzing Networks of Molecules Assembled by Structural Similarity. 2429-2443
• 
  Xia Ning, Huzefa Rangwala, George Karypis:
  Multi-Assay-Based Structure-Activity Relationship Models: Improving Structure-Activity Relationship Models by Incorporating Activity Information from Related Targets. 2444-2456
• 
  Laura Delgado-Soler, Raúl Toral, Maria Santos Tomás, Jaime Rubio-Martinez:
  RED: A Set of Molecular Descriptors Based on Re'nyi Entropy. 2457-2468
• 
  Boaz Musafia, Hanoch Senderowitz:
  Bioactive Conformational Biasing: A New Method for Focusing Conformational Ensembles on Bioactive-Like Conformers. 2469-2480
• 
  Pavel G. Polishchuk, Eugene N. Muratov, Anatoly G. Artemenko, Oleg G. Kolumbin, Nail N. Muratov, Victor Kuzmin:
  Application of Random Forest Approach to QSAR Prediction of Aquatic Toxicity. 2481-2488
• 
  Simone Brogi, Maria Kladi, Constantinos Vagias, Panagiota Papazafiri, Vassilios Roussis, Andrea Tafi:
  Pharmacophore Modeling for Qualitative Prediction of Antiestrogenic Activity. 2489-2497
• 
  R. S. K. Vijayan, Indrani Bera, Prabu Manoharan, Sangita Saha, Nanda Ghoshal:
  Combinatorial Library Enumeration and Lead Hopping using Comparative Interaction Fingerprint Analysis and Classical 2D QSAR Methods for Seeking Novel GABA_A α₃ Modulators. 2498-2511
• 
  Hao Fan, John J. Irwin, Benjamin M. Webb, Gerhard Klebe, Brian K. Shoichet, Andrej Sali:
  Molecular Docking Screens Using Comparative Models of Proteins. 2512-2527
• 
  Minkyoung Kim, Seung-Hoon Choi, Junhyoung Kim, Kihang Choi, Jae-Min Shin, Sang-Kee Kang, Yun-Jaie Choi, Dong Hyun Jung:
  Density-Based Clustering of Small Peptide Conformations Sampled from a Molecular Dynamics Simulation. 2528-2536
• 
  Sayan Ranu, Ambuj K. Singh:
  Mining Statistically Significant Molecular Substructures for Efficient Molecular Classification. 2537-2550
• 
  Lars Carlsson, Ernst Ahlberg Helgee, Scott Boyer:
  Interpretation of Nonlinear QSAR Models Applied to Ames Mutagenicity Data. 2551-2558
• 
  Ernst Ahlberg Helgee, Lars Carlsson, Scott Boyer:
  A Method for Automated Molecular Optimization Applied to Ames Mutagenicity Data. 2559-2563
• 
  Pablo Englebienne, Nicolas Moitessier:
  Docking Ligands into Flexible and Solvated Macromolecules. 5. Force-Field-Based Prediction of Binding Affinities of Ligands to Proteins. 2564-2571
• 
  Mark Hewitt, Mark T. D. Cronin, Steven J. Enoch, Judith C. Madden, David W. Roberts, John C. Dearden:
  In Silico Prediction of Aqueous Solubility: The Solubility Challenge. 2572-2587
• 
  Lisa Michielan, Lothar Terfloth, Johann Gasteiger, Stefano Moro:
  Comparison of Multilabel and Single-Label Classification Applied to the Prediction of the Isoform Specificity of Cytochrome P450 Substrates. 2588-2605
• 
  Napoleão Fonseca Valadares, Lívia Barros Salum, Igor Polikarpov, Adriano D. Andricopulo, Richard Garratt:
  Role of Halogen Bonds in Thyroid Hormone Receptor Selectivity: Pharmacophore-Based 3D-QSSR Studies. 2606-2616
• 
  Matthew Clark, Jeffrey S. Wiseman:
  Fragment-Based Prediction of the Clinical Occurrence of Long QT Syndrome and Torsade de Pointes. 2617-2626
• 
  Ambarnil Ghosh, Ashesh Nandy, Papiya Nandy, Brian D. Gute, Subhash C. Basak:
  Computational Study of Dispersion and Extent of Mutated and Duplicated Sequences of the H5N1 Influenza Neuraminidase over the Period 1997-2008. 2627-2638

Volume 49, Number 12, December 2009

Chemical Information

• 
  Marian D. Brodney, Arthur D. Brosius, Tracy Gregory, Steven D. Heck, Jacquelyn L. Klug-McLeod, Christopher S. Poss:
  Project-Focused Activity and Knowledge Tracker: A Unified Data Analysis, Collaboration, and Workflow Tool for Medicinal Chemistry Project Teams. 2639-2649
• 
  Megumi Ikemori-Kawada, Takatoshi Kawai, Masaki Goto, Yuan John Wang, Yoshiyuki Kawakami:
  Conformational Analyses and MO Studies of f152A1 and Its Analogues as Potent Protein Kinase Inhibitors. 2650-2659
• 
  Ralph Kühne, Ralf-Uwe Ebert, Gerrit Schüürmann:
  Chemical Domain of QSAR Models from Atom-Centered Fragments. 2660-2669
• 
  Anirban Misra, Thomas G. Schmalz, Douglas J. Klein:
  Clar Theory for Radical Benzenoids. 2670-2676

Computational Chemistry

• 
  Naoki Tanaka, Kazuki Ohno, Tatsuya Niimi, Ayako Moritomo, Kenichi Mori, Masaya Orita:
  Small-World Phenomena in Chemical Library Networks: Application to Fragment-Based Drug Discovery. 2677-2686
• 
  S. Nehru Viji, Arun Prasad Pandurangan, Gautham Namasivayam:
  Protein-Ligand Docking Using Mutually Orthogonal Latin Squares (MOLSDOCK). 2687-2694
• 
  Jitender Verma, Alpeshkumar K. Malde, Santosh A. Khedkar, Radhakrishnan P. Iyer, Evans C. Coutinho:
  Local Indices for Similarity Analysis (LISA) - A 3D-QSAR Formalism Based on Local Molecular Similarity. 2695-2707
• 
  Fergal P. Casey, Emilie Pihan, Denis C. Shields:
  Discovery of Small Molecule Inhibitors of Protein-Protein Interactions Using Combined Ligand and Target Score Normalization. 2708-2717
• 
  Quan Liao, Ji-Bo Wang, Yue W. Webster, Ian A. Watson:
  GPU Accelerated Support Vector Machines for Mining High-Throughput Screening Data. 2718-2725

Computational Biochemistry

• 
  Ting-Lan Chiu, Jonathan Solberg, Satish Patil, Todd W. Geders, Xia Zhang, Subhashree Rangarajan, Rawle Francis, Barry C. Finzel, Michael A. Walters, Derek J. Hook, Elizabeth A. Amin:
  Identification of Novel Non-Hydroxamate Anthrax Toxin Lethal Factor Inhibitors by Topomeric Searching, Docking and Scoring, and in Vitro Screening. 2726-2734
• 
  Jin Woo Park, Won Ho Jo:
  Infiltration of Water Molecules into the Oseltamivir-Binding Site of H274Y Neuraminidase Mutant Causes Resistance to Oseltamivir. 2735-2741
• 
  Tuomo Kalliokoski, Heikki S. Salo, Maija Lahtela-Kakkonen, Antti Poso:
  The Effect of Ligand-Based Tautomer and Protomer Prediction on Structure-Based Virtual Screening. 2742-2748
• 
  Mark Agostino, Cassandra Jene, Tristan Boyle, Paul A. Ramsland, Elizabeth Yuriev:
  Molecular Docking of Carbohydrate Ligands to Antibodies: Structural Validation against Crystal Structures. 2749-2760

Pharmaceutical Modeling

• 
  Eleanor J. Gardiner, David A. Cosgrove, Robin Taylor, Valerie J. Gillet:
  Multiobjective Optimization of Pharmacophore Hypotheses: Bias Toward Low-Energy Conformations. 2761-2773
• 
  Gabriella Ortore, Francesco Di Colo, Adriano Martinelli:
  Docking of Hydroxamic Acids into HDAC1 and HDAC8: A Rationalization of Activity Trends and Selectivities. 2774-2785
• 
  Gary Tresadern, Dimitris K. Agrafiotis:
  Conformational Sampling with Stochastic Proximity Embedding and Self-Organizing Superimposition: Establishing Reasonable Parameters for Their Practical Use. 2786-2800
• 
  Chenzhong Liao, Marc C. Nicklaus:
  Comparison of Nine Programs Predicting pK_a Values of Pharmaceutical Substances. 2801-2812
• 
  Janet L. Paulsen, Amy C. Anderson:
  Scoring Ensembles of Docked Protein: Ligand Interactions for Virtual Lead Optimization. 2813-2819
• 
  Lisa Michielan, Stephanie Federico, Lothar Terfloth, Dimitar Hristozov, Barbara Cacciari, Karl Norbert Klotz, Giampiero Spalluto, Johann Gasteiger, Stefano Moro:
  Exploring Potency and Selectivity Receptor Antagonist Profiles Using a Multilabel Classification Approach: The Human Adenosine Receptors as a Key Study. 2820-2836
• 
  Julen Oyarzabal, Joaquin Pastor, Trevor J. Howe:
  Optimizing the Performance of In Silico ADMET General Models According to Local Requirements: MARS Approach. Solubility Estimations As Case Study. 2837-2850
• 
  Debananda Das, Yasuhiro Koh, Yasushi Tojo, Arun K. Ghosh, Hiroaki Mitsuya:
  Prediction of Potency of Protease Inhibitors Using Free Energy Simulations with Polarizable Quantum Mechanics-Based Ligand Charges and a Hybrid Water Model. 2851-2862

Bioinformatics

• 
  Sourav Das, Arshad Kokardekar, Curt M. Breneman:
  Rapid Comparison of Protein Binding Site Surfaces with Property Encoded Shape Distributions. 2863-2872
• 
  Davor Juretic, Damir Vukicevic, Nada Ilic, Nikolinka Antcheva, Alessandro Tossi:
  Computational Design of Highly Selective Antimicrobial Peptides. 2873-2882

Software Description

• 
  Vladimir V. Diky, Robert D. Chirico, Andrei F. Kazakov, Chris Muzny, Michael Frenkel:
  ThermoData Engine (TDE): Software Implementation of the Dynamic Data Evaluation Concept. 4. Chemical Reactions. 2883-2896

Computer Software Reviews

• 
  Jonathan M. Goodman:
  Computer Software Review: Reaxys. 2897-2898