Journal of Chemical Information and Modeling, Volume 48

Volume 48, Number 1, January 2008

Perspective

• 
  Ken A. Brameld, Bernd Kuhn, Deborah C. Reuter, Martin Stahl:
  Small Molecule Conformational Preferences Derived from Crystal Structure Data. A Medicinal Chemistry Focused Analysis. 1-24

Letter

• 
  Stephen R. Johnson:
  The Trouble with QSAR (or How I Learned To Stop Worrying and Embrace Fallacy). 25-26

Chemical Information

• 
  Puneet Sharma, Srinivasa M. Salapaka, Carolyn L. Beck:
  A Scalable Approach to Combinatorial Library Design for Drug Discovery. 27-41
• 
  Pallav D. Patel, Maulik R. Patel, Neerja Kaushik-Basu, Tanaji T. Talele:
  3D QSAR and Molecular Docking Studies of Benzimidazole Derivatives as Hepatitis C Virus NS5B Polymerase Inhibitors. 42-55
• 
  Dimitar Hristozov, Johann Gasteiger, Fernando B. Da Costa:
  Multilabeled Classification Approach To Find a Plant Source for Terpenoids. 56-67
• 
  Peter Ertl, Silvio Roggo, Ansgar Schuffenhauer:
  Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries. 68-74
• 
  Yuan Wang, Jürgen Bajorath:
  Balancing the Influence of Molecular Complexity on Fingerprint Similarity Searching. 75-84

Computational Chemistry

• 
  Mírian S. C. Pereira, Rudolf Kiralj, Márcia M. C. Ferreira:
  Theoretical Study of Radical and Neutral Intermediates of Artemisinin Decomposition. 85-98
• 
  Kanda Nivesanond, Anik Peeters, Dirk Lamoen, Christian Van Alsenoy:
  Conformational Analysis of TMC114, a Novel HIV-1 Protease Inhibitor. 99-108
• 
  Ray M. Marín, Nestor F. Aguirre, Edgar E. Daza:
  Graph Theoretical Similarity Approach To Compare Molecular Electrostatic Potentials. 109-118
• 
  Benjamin Folch, Marianne Rooman, Yves Dehouck:
  Thermostability of Salt Bridges versus Hydrophobic Interactions in Proteins Probed by Statistical Potentials. 119-127
• 
  Yegor D. Smurnyy, Kirill A. Blinov, Tatiana S. Churanova, Mikhail E. Elyashberg, Antony J. Williams:
  Toward More Reliable ¹³C and ¹H Chemical Shift Prediction: A Systematic Comparison of Neural-Network and Least-Squares Regression Based Approaches. 128-134
• 
  Kazunari Hattori, Hiroaki Wakabayashi, Kenta Tamaki:
  Predicting Key Example Compounds in Competitors' Patent Applications Using Structural Information Alone. 135-142
• 
  Zoran Markovic, Svetlana Markovic:
  Last Step of the Para Route of the Kolbe-Schmitt Reaction. 143-147
• 
  Yoshifumi Fukunishi, Haruki Nakamura:
  Improvement of Protein-Compound Docking Scores by Using Amino-Acid Sequence Similarities of Proteins. 148-156
• 
  Matthieu Montès, Emmanuelle Braud, Maria A. Miteva, Mary-Lorène Goddard, Odile Mondésert, Stéphanie Kolb, Marie-Priscille Brun, Bernard Ducommun, Christiane Garbay, Bruno O. Villoutreix:
  Receptor-Based Virtual Ligand Screening for the Identification of Novel CDC25 Phosphatase Inhibitors. 157-165
• 
  Paul Watson:
  Naïve Bayes Classification Using 2D Pharmacophore Feature Triplet Vectors. 166-178
• 
  Mohamed Diwan M. AbdulHameed, Adel Hamza, Junjun Liu, Xiaoqin Huang, Chang-Guo Zhan:
  Human Microsomal Prostaglandin E Synthase-1 (mPGES-1) Binding with Inhibitors and the Quantitative Structure-Activity Correlation. 179-185

Pharmaceutical Modeling

• 
  Jörn Marialke, Simon Tietze, Joannis Apostolakis:
  Similarity Based Docking. 186-196
• 
  Hye-Jung Kim, Munikumar Reddy Doddareddy, Hyunah Choo, Yong Seo Cho, Kyoung Tai No, Woo-Kyu Park, Ae Nim Pae:
  New Serotonin 5-HT₆ Ligands from Common Feature Pharmacophore Hypotheses. 197-206
• 
  Takanori Ohgaru, Ryo Shimizu, Kousuke Okamoto, Masaya Kawase, Yuko Shirakuni, Rika Nishikiori, Tatsuya Takagi:
  Ordinal Classification Using Comparative Molecular Field Analysis. 207-212
• 
  Mariana Boiani, Hugo Cerecetto, Mercedes González, Johann Gasteiger:
  Modeling anti-Trypanosoma cruzi Activity of N-Oxide Containing Heterocycles. 213-219
• 
  Laura D. Hughes, David S. Palmer, Florian Nigsch, John B. O. Mitchell:
  Why Are Some Properties More Difficult To Predict than Others? A Study of QSPR Models of Solubility, Melting Point, and Log P. 220-232
• 
  Simon Birksø Larsen, Flemming Steen Jørgensen, Lars Olsen:
  QSAR Models for the Human H⁺/Peptide Symporter, hPEPT1: Affinity Prediction Using Alignment-Independent Descriptors. 233-241

Computer Software Reviews

• 
  Wendy A. Warr:
  EndNote X (and XI) for Windows. 242-244

Book Reviews

• 
  Stephen R. Heller:
  Adobe Acrobat 8: Classroom in a Book By the Adobe Creative Team. Adobe Press. 2006. xii + 514 pp, CD-ROM. ISBN 0-321-47085-0, 978-0-321-47085-0. Softcover U.S. $45.00. 245
• 
  Stephen R. Heller:
  Maya 8 for Windows and Macintosh (Visual Quickstart Guide) By Morgan Robinson & Nathaniel Stern. Peachpit Press. 2007. xii + 532 pp. ISBN 0-321-47675-1, 978-0-321-47675-1. Softcover U.S. $34.99. 245

Errata

• 
  Timothy Lovell, Hongming Chen, Paul D. Lyne, Fabrizio Giordanetto, Jin Li:
  On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors. [J. Chem. Inf. Model. 46, 401-415 (2006)]. 246

Volume 48, Number 2, February 2008

Chemical Information

• 
  Martin Vogt, Jürgen Bajorath:
  Bayesian Similarity Searching in High-Dimensional Descriptor Spaces Combined with Kullback-Leibler Descriptor Divergence Analysis. 247-255
• 
  Brian B. Masek, Lingling Shen, Karl M. Smith, Robert S. Pearlman:
  Sharing Chemical Information without Sharing Chemical Structure. 256-261

Computational Chemistry

• 
  Daniel J. Scott, Steven Manos, Peter V. Coveney:
  Design of Electroceramic Materials Using Artificial Neural Networks and Multiobjective Evolutionary Algorithms. 262-273
• 
  Martin Holena, Tatjana Cukic, Uwe Rodemerck, David Linke:
  Optimization of Catalysts Using Specific, Description-Based Genetic Algorithms. 274-282
• 
  Jernej Zidar, Elizabeta T. Pirc, Milan Hodoscek, Peter Bukovec:
  Copper(II) Ion Binding to Cellular Prion Protein. 283-287
• 
  Reiji Teramoto, Hiroaki Fukunishi:
  Consensus Scoring with Feature Selection for Structure-Based Virtual Screening. 288-295
• 
  Stuart Firth-Clark, Stewart B. Kirton, Henriëtte M. G. Willems, Anthony Williams:
  De Novo Ligand Design to Partially Flexible Active Sites: Application of the ReFlex Algorithm to Carboxypeptidase A, Acetylcholinesterase, and the Estrogen Receptor. 296-305
• 
  Florian Nigsch, John B. O. Mitchell:
  How To Winnow Actives from Inactives: Introducing Molecular Orthogonal Sparse Bigrams (MOSBs) and Multiclass Winnow. 306-318
• 
  Steffen Renner, Swetlana Derksen, Sebastian Radestock, Fabian Mörchen:
  Maximum Common Binding Modes (MCBM): Consensus Docking Scoring Using Multiple Ligand Information and Interaction Fingerprints. 319-332

Computational Biochemistry

• 
  Francisco Rodríguez-Ropero, David Zanuy, Jordi Casanovas, Ruth Nussinov, Carlos Alemán:
  Application of 1-Aminocyclohexane Carboxylic Acid to Protein Nanostructure Computer Design. 333-343
• 
  James R. Trudell, Minerva E. Yue, Edward J. Bertaccini, Andrew Jenkins, Neil L. Harrison:
  Molecular Modeling and Mutagenesis Reveals a Tetradentate Binding Site for Zn²⁺ in GABA_A αβ Receptors and Provides a Structural Basis for the Modulating Effect of the γ Subunit. 344-349
• 
  Lisa Michielan, Magdalena Bacilieri, Andrea Schiesaro, Chiara Bolcato, Giorgia Pastorin, Giampiero Spalluto, Barbara Cacciari, Karl Norbert Klotz, Chosei Kaseda, Stefano Moro:
  Linear and Nonlinear 3D-QSAR Approaches in Tandem with Ligand-Based Homology Modeling as a Computational Strategy To Depict the Pyrazolo-Triazolo-Pyrimidine Antagonists Binding Site of the Human Adenosine A_2A Receptor. 350-363

Pharmaceutical Modeling

• 
  Fumiyoshi Yamashita, Hideto Hara, Takayuki Ito, Mitsuru Hashida:
  Novel Hierarchical Classification and Visualization Method for Multiobjective Optimization of Drug Properties: Application to Structure-Activity Relationship Analysis of Cytochrome P450 Metabolism. 364-369
• 
  Dmitry A. Konovalov, Nigel Sim, Eric Deconinck, Yvan Vander Heyden, Danny Coomans:
  Statistical Confidence for Variable Selection in QSAR Models via Monte Carlo Cross-Validation. 370-383
• 
  Alexander Hillebrecht, Gerhard Klebe:
  Use of 3D QSAR Models for Database Screening: A Feasibility Study. 384-396
• 
  Benjamin C. Roberts, Ricardo L. Mancera:
  Ligand-Protein Docking with Water Molecules. 397-408
• 
  Fanny Bonachéra, Dragos Horvath:
  Fuzzy Tricentric Pharmacophore Fingerprints. 2. Application of Topological Fuzzy Pharmacophore Triplets in Quantitative Structure-Activity Relationships. 409-425
• 
  Robert P. Sheridan:
  Alternative Global Goodness Metrics and Sensitivity Analysis: Heuristics to Check the Robustness of Conclusions from Studies Comparing Virtual Screening Methods. 426-433

Bioinformatics

• 
  Guillermín Agüero-Chapín, Humberto González Díaz, Gustavo de la Riva, Edrey Rodríguez, Aminael Sánchez-Rodríguez, Gianni Podda, Roberto I. Vazquez-Padrón:
  MMM-QSAR Recognition of Ribonucleases without Alignment: Comparison with an HMM Model and Isolation from Schizosaccharomyces pombe, Prediction, and Experimental Assay of a New Sequence. 434-448

Software Description

• 
  Daniel J. Scott, Steven Manos, Peter V. Coveney, Jeremy C. H. Rossiny, Sarah Fearn, John A. Kilner, Robert C. Pullar, Neil Mc N. Alford, A.-K. Axelsson, Yong Zhang, Lifeng Chen, Shoufeng Yang, Julian R. G. Evans, M. T. Sebastian:
  Functional Ceramic Materials Database: An Online Resource for Materials Research. 449-455
• 
  Rajarshi Guha:
  Flexible Web Service Infrastructure for the Development and Deployment of Predictive Models. 456-464

Volume 48, Number 3, March 2008

Chemical Information

• 
  Xiang-Qun Xie, Jian-zhong Chen:
  Data Mining a Small Molecule Drug Screening Representative Subset from NIH PubChem. 465-475
• 
  Sune Askjaer, Morten Langgård:
  Combining Pharmacophore Fingerprints and PLS-Discriminant Analysis for Virtual Screening and SAR Elucidation. 476-488
• 
  Hui Sun Lee, Jiwon Choi, Irina Kufareva, Ruben Abagyan, Anton V. Filikov, Young Yang, Sukjoon Yoon:
  Optimization of High Throughput Virtual Screening by Combining Shape-Matching and Docking Methods. 489-497
• 
  Maciej Haranczyk, John D. Holliday:
  Comparison of Similarity Coefficients for Clustering and Compound Selection. 498-508
• 
  Violeta I. Pérez-Nueno, David W. Ritchie, Obdulia Rabal, Rosalia Pascual, José I. Borrell, Jordi Teixidó:
  Comparison of Ligand-Based and Receptor-Based Virtual Screening of HIV Entry Inhibitors for the CXCR4 and CCR5 Receptors Using 3D Ligand Shape Matching and Ligand-Receptor Docking. 509-533

Computational Chemistry

• 
  Hiromasa Kaneko, Masamoto Arakawa, Kimito Funatsu:
  Development of a New Regression Analysis Method Using Independent Component Analysis. 534-541
• 
  Ruifeng Liu, Diansong Zhou:
  Using Molecular Fingerprint as Descriptors in the QSPR Study of Lipophilicity. 542-549
• 
  K. A. Blinov, Y. D. Smurnyy, M. E. Elyashberg, T. S. Churanova, M. Kvasha, Christoph Steinbeck, B. A. Lefebvre, A. J. Williams:
  Performance Validation of Neural Network Based ¹³C NMR Prediction Using a Publicly Available Data Source. 550-555
• 
  Aleksandr V. Marenich, Pei-Han Yong, Isaac B. Bersuker, James E. Boggs:
  Quantitative Antidiabetic Activity Prediction for the Class of Guanidino- and Aminoguanidinopropionic Acid Analogs Based on Electron-Conformational Studies. 556-568

Computational Biochemistry

• 
  Natalia Artemenko:
  Distance Dependent Scoring Function for Describing Protein-Ligand Intermolecular Interactions. 569-574
• 
  Hiroaki Fukunishi, Reiji Teramoto, Jiro Shimada:
  Hidden Active Information in a Random Compound Library: Extraction Using a Pseudo-Structure-Activity Relationship Model. 575-582
• 
  Junichi Goto, Ryoichi Kataoka, Hajime Muta, Noriaki Hirayama:
  ASEDock-Docking Based on Alpha Spheres and Excluded Volumes. 583-590
• 
  Wonseok Oh, Doo Nam Kim, Jihoon Jung, Kwang-Hwi Cho, Kyoung Tai No:
  New Combined Model for the Prediction of Regioselectivity in Cytochrome P450/3A4 Mediated Metabolism. 591-601

Pharmaceutical Modeling

• 
  Markus H. J. Seifert:
  Optimizing the Signal-to-Noise Ratio of Scoring Functions for Protein-Ligand Docking. 602-612
• 
  Nadine Schneider, Christine Jäckels, Claudia Andres, Michael C. Hutter:
  Gradual in Silico Filtering for Druglike Substances. 613-628
• 
  Raphaël Frédérick, William A. Denny:
  Phosphoinositide-3-kinases (PI3Ks): Combined Comparative Modeling and 3D-QSAR To Rationalize the Inhibition of p110α. 629-638
• 
  Wesley H. Brooks, Kenyon G. Daniel, Shen-Shu Sung, Wayne C. Guida:
  Computational Validation of the Importance of Absolute Stereochemistry in Virtual Screening. 639-645
• 
  Rajarshi Guha, John H. Van Drie:
  Structure-Activity Landscape Index: Identifying and Quantifying Activity Cliffs. 646-658
• 
  José S. Duca, Vincent S. Madison, Johannes H. Voigt:
  Cross-Docking of Inhibitors into CDK2 Structures. 1. 659-668
• 
  Johannes H. Voigt, Carl Elkin, Vincent S. Madison, José S. Duca:
  Cross-Docking of Inhibitors into CDK2 Structures. 2. 669-678
• 
  Fabian Dey, Amedeo Caflisch:
  Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization. 679-690

Volume 48, Number 4, April 2008

Chemical Information

• 
  Muthukumarasamy Karthikeyan, Subramanian Krishnan, Anil Kumar Pandey, Andreas Bender, Alexander Tropsha:
  Distributed Chemical Computing Using ChemStar: An Open Source Java Remote Method Invocation Architecture Applied to Large Scale Molecular Data from PubChem. 691-703
• 
  Sebastian G. Rohrer, Knut Baumann:
  Impact of Benchmark Data Set Topology on the Validation of Virtual Screening Methods: Exploration and Quantification by Spatial Statistics. 704-718
• 
  Kirstin Moffat, Valerie J. Gillet, Martin Whittle, Gianpaolo Bravi, Andrew R. Leach:
  A Comparison of Field-Based Similarity Searching Methods: CatShape, FBSS, and ROCS. 719-729
• 
  Nikil Wale, Ian A. Watson, George Karypis:
  Indirect Similarity Based Methods for Effective Scaffold-Hopping in Chemical Compounds. 730-741
• 
  Hanna Geppert, Tamás Horváth, Thomas Gärtner, Stefan Wrobel, Jürgen Bajorath:
  Support-Vector-Machine-Based Ranking Significantly Improves the Effectiveness of Similarity Searching Using 2D Fingerprints and Multiple Reference Compounds. 742-746
• 
  Reiji Teramoto, Hiroaki Fukunishi:
  Structure-Based Virtual Screening with Supervised Consensus Scoring: Evaluation of Pose Prediction and Enrichment Factors. 747-754
• 
  Jérôme Hert, Michael J. Keiser, John J. Irwin, Tudor I. Oprea, Brian K. Shoichet:
  Quantifying the Relationships among Drug Classes. 755-765

Computational Chemistry

• 
  Hao Zhu, Alexander Tropsha, Denis Fourches, Alexandre Varnek, Ester Papa, Paola Gramatica, Tomas Öberg, Phuong Dao, Artem Cherkasov, Igor V. Tetko:
  Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis. 766-784
• 
  Anton Schwaighofer, Timon Schroeter, Sebastian Mika, Katja Hansen, Antonius ter Laak, Philip Lienau, Andreas Reichel, Nikolaus Heinrich, Klaus-Robert Müller:
  A Probabilistic Approach to Classifying Metabolic Stability. 785-796
• 
  Modest von Korff, Joël Freyss, Thomas Sander:
  Flexophore, a New Versatile 3D Pharmacophore Descriptor That Considers Molecular Flexibility. 797-810
• 
  Drew Bullard, Alberto Gobbi, Matthew A. Lardy, Charles Perkins, Zach Little:
  Hydra: A Self Regenerating High Performance Computing Grid for Drug Discovery. 811-816
• 
  David C. Sullivan, Eric J. Martin:
  Exploiting Structure-Activity Relationships in Docking. 817-830

Computational Biochemistry

• 
  Mansour H. Almatarneh, Christopher G. Flinn, Raymond A. Poirier:
  Mechanisms for the Deamination Reaction of Cytosine with H₂O/OH^- and 2H₂O/OH^-: A Computational Study. 831-843
• 
  Federico M. Ruiz, Rubén Gil-Redondo, Antonio Morreale, Angel R. Ortiz, Carmen Fàbrega, Jerónimo Bravo:
  Structure-Based Discovery of Novel Non-nucleosidic DNA Alkyltransferase Inhibitors: Virtual Screening and in Vitro and in Vivo Activities. 844-854
• 
  Edward J. Bertaccini, Erik Lindahl, Titia Sixma, James R. Trudell:
  Effect of Cobratoxin Binding on the Normal Mode Vibration within Acetylcholine Binding Protein. 855-860

Pharmaceutical Modeling

• 
  Eric J. Martin, David C. Sullivan:
  AutoShim: Empirically Corrected Scoring Functions for Quantitative Docking with a Crystal Structure and IC₅₀ Training Data. 861-872
• 
  Eric J. Martin, David C. Sullivan:
  Surrogate AutoShim: Predocking into a Universal Ensemble Kinase Receptor for Three Dimensional Activity Prediction, Very Quickly, without a Crystal Structure. 873-881
• 
  Thomas R. Webb, Ruben E. Venegas, Jian Wang, Alain Deschênes:
  Generation of New Synthetic Scaffolds Using Framework Libraries Selected and Refined via Medicinal Chemist Synthetic Expertise. 882-888
• 
  Jerry Osagie Ebalunode, Zheng Ouyang, Jie Liang, Weifan Zheng:
  Novel Approach to Structure-Based Pharmacophore Search Using Computational Geometry and Shape Matching Techniques. 889-901
• 
  Christopher R. Corbeil, Pablo Englebienne, Constantin G. Yannopoulos, Laval Chan, Sanjoy K. Das, Darius Bilimoria, Lucille L'Heureux, Nicolas Moitessier:
  Docking Ligands into Flexible and Solvated Macromolecules. 2. Development and Application of Fitted 1.5 to the Virtual Screening of Potential HCV Polymerase Inhibitors. 902-909
• 
  Takanori Ohgaru, Ryo Shimizu, Kousuke Okamoto, Norihito Kawashita, Masaya Kawase, Yuko Shirakuni, Rika Nishikiori, Tatsuya Takagi:
  Enhancement of Ordinal CoMFA by Ridge Logistic Partial Least Squares. 910-917
• 
  Rafael V. C. Guido, Glaucius Oliva, Carlos Alberto Montanari, Adriano D. Andricopulo:
  Structural Basis for Selective Inhibition of Trypanosomatid Glyceraldehyde-3-Phosphate Dehydrogenase: Molecular Docking and 3D QSAR Studies. 918-929

Bioinformatics

• 
  Yukiko Fujiwara, Yoshiko Yamashita, Tsutomu Osoda, Minoru Asogawa, Chiaki Fukushima, Masaaki Asao, Hideshi Shimadzu, Kazuya Nakao, Ryo Shimizu:
  Virtual Screening System for Finding Structurally Diverse Hits by Active Learning. 930-940

Volume 48, Number 5, May 2008

Chemical Information

• 
  Steven W. Muchmore, Derek A. Debe, James T. Metz, Scott P. Brown, Yvonne C. Martin, Philip J. Hajduk:
  Application of Belief Theory to Similarity Data Fusion for Use in Analog Searching and Lead Hopping. 941-948

Computational Chemistry

• 
  Kazuhisa Tsunoyama, Ata Amini, Michael J. E. Sternberg, Stephen H. Muggleton:
  Scaffold Hopping in Drug Discovery Using Inductive Logic Programming. 949-957
• 
  Cristiano Ruch Werneck Guimarães, Mario G. Cardozo:
  MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization. 958-970
• 
  Romualdo Benigni, Cecilia Bossa:
  Predictivity of QSAR. 971-980
• 
  Diansong Zhou, Yun Alelyunas, Ruifeng Liu:
  Scores of Extended Connectivity Fingerprint as Descriptors in QSPR Study of Melting Point and Aqueous Solubility. 981-987

Computational Biochemistry

• 
  Hiroaki Fukunishi, Reiji Teramoto, Toshikazu Takada, Jiro Shimada:
  Bootstrap-Based Consensus Scoring Method for Protein-Ligand Docking. 988-996
• 
  Xiang S. Wang, Hao Tang, Alexander Golbraikh, Alexander Tropsha:
  Combinatorial QSAR Modeling of Specificity and Subtype Selectivity of Ligands Binding to Serotonin Receptors 5HT1E and 5HT1F. 997-1013
• 
  Esther Kellenberger, Nicolas Foata, Didier Rognan:
  Ranking Targets in Structure-Based Virtual Screening of Three-Dimensional Protein Libraries: Methods and Problems. 1014-1025

Pharmaceutical Modeling

• 
  Prasenjit Mukherjee, Prashant V. Desai, Anuradha Srivastava, Babu L. Tekwani, Mitchell A. Avery:
  Probing the Structures of Leishmanial Farnesyl Pyrophosphate Synthases: Homology Modeling and Docking Studies. 1026-1040
• 
  Andrei Anghelescu, Robert Kirk DeLisle, Jeffrey F. Lowrie, Anthony E. Klon, Xiaoming Xie, David J. Diller:
  Technique for Generating Three-Dimensional Alignments of Multiple Ligands from One-Dimensional Alignments. 1041-1054
• 
  Mala L. Radhakrishnan, Bruce Tidor:
  Optimal Drug Cocktail Design: Methods for Targeting Molecular Ensembles and Insights from Theoretical Model Systems. 1055-1073
• 
  Jihoon Jung, Nam Doo Kim, Su Yeon Kim, Inhee Choi, Kwang-Hwi Cho, Wonseok Oh, Doo Nam Kim, Kyoung Tai No:
  Regioselectivity Prediction of CYP1A2-Mediated Phase I Metabolism. 1074-1080
• 
  David C. Thompson, Christine Humblet, Diane Joseph-McCarthy:
  Investigation of MM-PBSA Rescoring of Docking Poses. 1081-1091
• 
  Zaheer-ul-Haq, Reaz Uddin, Hongbin Yuan, Pavel A. Petukhov, Mohammad Iqbal Choudhary, Jeffry D. Madura:
  Receptor-Based Modeling and 3D-QSAR for a Quantitative Production of the Butyrylcholinesterase Inhibitors Based on Genetic Algorithm. 1092-1103
• 
  Sebastian Radestock, Tanja Weil, Steffen Renner:
  Homology Model-Based Virtual Screening for GPCR Ligands Using Docking and Target-Biased Scoring. 1104-1117

Bioinformatics

• 
  Andrzej Galat:
  Functional Drift of Sequence Attributes in the FK506-Binding Proteins (FKBPs). 1118-1130

Volume 48, Number 6, June 2008

Chemical Information

• 
  Tuomo Kalliokoski, Toni Rönkkö, Antti Poso:
  FieldChopper, A New Tool for Automatic Model Generation and Virtual Screening Based on Molecular Fields. 1131-1137
• 
  Ryan W. Benz, S. Joshua Swamidass, Pierre Baldi:
  Discovery of Power-Laws in Chemical Space. 1138-1151
• 
  Kentaro Kawai, Satoshi Fujishima, Yoshimasa Takahashi:
  Predictive Activity Profiling of Drugs by Topological-Fragment-Spectra-Based Support Vector Machines. 1152-1160
• 
  Eugen Lounkine, Jürgen Bajorath:
  Core Trees and Consensus Fragment Sequences for Molecular Representation and Similarity Analysis. 1161-1166

Computational Chemistry

• 
  John Manchester, Ryszard Czerminski:
  SAMFA: Simplifying Molecular Description for 3D-QSAR. 1167-1173
• 
  Tomasz Puzyn, Noriyuki Suzuki, Maciej Haranczyk, Janusz Rak:
  Calculation of Quantum-Mechanical Descriptors for QSPR at the DFT Level: Is It Necessary? 1174-1180

Computational Biochemistry

• 
  Robert Körner, Joannis Apostolakis:
  Automatic Determination of Reaction Mappings and Reaction Center Information. 1. The Imaginary Transition State Energy Approach. 1181-1189
• 
  Joannis Apostolakis, Oliver Sacher, Robert Körner, Johann Gasteiger:
  Automatic Determination of Reaction Mappings and Reaction Center Information. 2. Validation on a Biochemical Reaction Database. 1190-1198
• 
  Balázs Jójárt, Robert Kiss, Béla Viskolcz, György M. Keserü:
  Activation Mechanism of the Human Histamine H4 Receptor - An Explicit Membrane Molecular Dynamics Simulation Study. 1199-1210

Pharmaceutical Modeling

• 
  Orazio Nicolotti, Teresa Fabiola Miscioscia, Andrea Carotti, Francesco Leonetti, Angelo Carotti:
  An Integrated Approach to Ligand- and Structure-Based Drug Design: Development and Application to a Series of Serine Protease Inhibitors. 1211-1226
• 
  Xiao Hua Ma, R. Wang, S. Y. Yang, Z. R. Li, Ying Xue, Y. C. Wei, Boon Chuan Low, Yuzong Chen:
  Evaluation of Virtual Screening Performance of Support Vector Machines Trained by Sparsely Distributed Active Compounds. 1227-1237
• 
  Tao Zheng, Anton J. Hopfinger, Emilio Xavier Esposito, Jianzhong Liu, Yufeng J. Tseng:
  Membrane-Interaction Quantitative Structure-Activity Relationship (MI-QSAR) Analyses of Skin Penetration Enhancers. 1238-1256
• 
  Christophe Guilbert, Thomas L. James:
  Docking to RNA via Root-Mean-Square-Deviation-Driven Energy Minimization with Flexible Ligands and Flexible Targets. 1257-1268
• 
  Noel M. O'Boyle, Suzanne Clare Brewerton, Robin Taylor:
  Using Buriedness To Improve Discrimination between Actives and Inactives in Docking. 1269-1278

Bioinformatics

• 
  Nejc Carl, Janez Konc, Dusanka Janezic:
  Protein Surface Conservation in Binding Sites. 1279-1286

Computer Software Reviews

• 
  Gregory A. Reichard:
  SARVision Plus by ChemApps. 1287-1288

Volume 48, Number 7, July 2008

Chemical Information

• 
  Antonio Llinàs, Robert C. Glen, Jonathan M. Goodman:
  Solubility Challenge: Can You Predict Solubilities of 32 Molecules Using a Database of 100 Reliable Measurements? 1289-1303
• 
  Sara N. Pollock, Evangelos A. Coutsias, Michael J. Wester, Tudor I. Oprea:
  Scaffold Topologies. 1. Exhaustive Enumeration up to Eight Rings. 1304-1310
• 
  Michael J. Wester, Sara N. Pollock, Evangelos A. Coutsias, Tharun Kumar Allu, Sorel Muresan, Tudor I. Oprea:
  Scaffold Topologies. 2. Analysis of Chemical Databases. 1311-1324
• 
  Nahren Manuel Mascarenhas, Nanda Ghoshal:
  Combined Ligand and Structure Based Approaches for Narrowing on the Essential Physicochemical Characteristics for CDK4 Inhibition. 1325-1336
• 
  Huixiao Hong, Qian Xie, Weigong Ge, Feng Qian, Hong Fang, Leming Shi, Zhenqiang Su, Roger Perkins, Weida Tong:
  Mold², Molecular Descriptors from 2D Structures for Chemoinformatics and Toxicoinformatics. 1337-1344
• 
  Hiroki Fujiwara, Jiexun Wang, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu:
  Enumerating Treelike Chemical Graphs with Given Path Frequency. 1345-1357
• 
  Arkadiusz Ciesielski, Tadeusz Marek Krygowski, Michal Cyranski:
  Why Are the Kinked Polyacenes More Stable than the Straight Ones? A Topological Study and Introduction of a New Topological Index of Aromaticity. 1358-1366
• 
  Pierre Baldi, Daniel S. Hirschberg, Ramzi Nasr:
  Speeding Up Chemical Database Searches Using a Proximity Filter Based on the Logical Exclusive OR. 1367-1378
• 
  Adam C. Lee, Kerby Shedden, Gustavo R. Rosania, Gordon M. Crippen:
  Data Mining the NCI60 to Predict Generalized Cytotoxicity. 1379-1388
• 
  Ingo Vogt, Jürgen Bajorath:
  Design and Exploration of Target-Selective Chemical Space Representations. 1389-1395

Computational Chemistry

• 
  Caterina Barillari, Gilles Marcou, Didier Rognan:
  Hot-Spots-Guided Receptor-Based Pharmacophores (HS-Pharm): A Knowledge-Based Approach to Identify Ligand-Anchoring Atoms in Protein Cavities and Prioritize Structure-Based Pharmacophores. 1396-1410
• 
  Dilmurat Yusuf, Andrew M. Davis, Gerard J. Kleywegt, Stefan Schmitt:
  An Alternative Method for the Evaluation of Docking Performance: RSR vs RMSD. 1411-1422

Computational Biochemistry

• 
  Henri Xhaard, Vera Backstrom, Konstantin A. Denessiouk, Mark S. Johnson:
  Coordination of Na⁺ by Monoamine Ligands in Dopamine, Norepinephrine, and Serotonin Transporters. 1423-1437
• 
  Xiaoyu Zhao, Xiaofeng Liu, Yuanyuan Wang, Zhi Chen, Ling Kang, Hailei Zhang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Honglin Li, Xicheng Wang, Hualiang Jiang:
  An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA. 1438-1447

Pharmaceutical Modeling

• 
  Ian M. Withers, Michael P. Mazanetz, Hao Wang, Peter M. Fischer, Charles A. Laughton:
  Active Site Pressurization: A New Tool for Structure-Guided Drug Design and Other Studies of Protein Flexibility. 1448-1454
• 
  Aldo Jongejan, Herman D. Lim, Rogier A. Smits, Iwan J. P. de Esch, Eric E. J. Haaksma, Rob Leurs:
  Delineation of Agonist Binding to the Human Histamine H₄ Receptor Using Mutational Analysis, Homology Modeling, and ab Initio Calculations. 1455-1463
• 
  Mary Pat Beavers, Michael C. Myers, Parag P. Shah, Jeremy E. Purvis, Scott L. Diamond, Barry S. Cooperman, Donna M. Huryn, Amos B. Smith III:
  Molecular Docking of Cathepsin L Inhibitors in the Binding Site of Papain. 1464-1472
• 
  Andreas Schüller, Gisbert Schneider:
  Identification of Hits and Lead Structure Candidates with Limited Resources by Adaptive Optimization. 1473-1491

Bioinformatics

• 
  Stephan Raub, Andreas Steffen, Andreas Kämper, Christel M. Marian:
  AIScore Chemically Diverse Empirical Scoring Function Employing Quantum Chemical Binding Energies of Hydrogen-Bonded Complexes. 1492-1510

Software Description

• 
  Christopher P. Paolini, Subrata Bhattacharjee:
  A Web Service Infrastructure for Thermochemical Data. 1511-1523
• 
  Fergal P. Casey, Norman E. Davey, Ivan Baran, Radka Svobodová Vareková, Denis C. Shields:
  Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO). 1524-1529
• 
  Toon Verstraelen, Veronique Van Speybroeck, Michel Waroquier:
  ZEOBUILDER: A GUI Toolkit for the Construction of Complex Molecular Structures on the Nanoscale with Building Blocks. 1530-1541

Volume 48, Number 8, August 2008

Chemical Information

• 
  Kristian Birchall, Valerie J. Gillet, Gavin Harper, Stephen D. Pickett:
  Evolving Interpretable Structure-Activity Relationships. 1. Reduced Graph Queries. 1543-1557
• 
  Kristian Birchall, Valerie J. Gillet, Gavin Harper, Stephen D. Pickett:
  Evolving Interpretable Structure-Activity Relationship Models. 2. Using Multiobjective Optimization To Derive Multiple Models. 1558-1570
• 
  Jim Downing, Peter Murray-Rust, Alan P. Tonge, Peter B. Morgan, Henry S. Rzepa, Fiona Cotterill, Nick Day, Matt J. Harvey:
  SPECTRa: The Deposition and Validation of Primary Chemistry Research Data in Digital Repositories. 1571-1581

Computational Chemistry

• 
  Rozana Othman, Tan Siew Kiat, Norzulaani Khalid, Rohana Yusof, E. Irene Newhouse, James S. Newhouse, Masqudul Alam, Noorsaadah Abdul Rahman:
  Docking of Noncompetitive Inhibitors into Dengue Virus Type 2 Protease: Understanding the Interactions with Allosteric Binding Sites. 1582-1591
• 
  Mosé Casalegno, Guido Sello, Emilio Benfenati:
  Definition and Detection of Outliers in Chemical Space. 1592-1601
• 
  Patrick A. Holt, Jonathan B. Chaires, John O. Trent:
  Molecular Docking of Intercalators and Groove-Binders to Nucleic Acids Using Autodock and Surflex. 1602-1615
• 
  Andreas Kerzmann, Jan Fuhrmann, Oliver Kohlbacher, Dirk Neumann:
  BALLDock/SLICK: A New Method for Protein-Carbohydrate Docking. 1616-1625
• 
  W. Michael Brown, Ariella Sasson, Donald R. Bellew, Lucy A. Hunsaker, Shawn Martin, Andrei Leitão, Lorraine M. Deck, David L. Vander Jagt, Tudor I. Oprea:
  Efficient Calculation of Molecular Properties from Simulation Using Kernel Molecular Dynamics. 1626-1637
• 
  Thy-Hou Lin, Guan-Liang Lin:
  An Anchor-Dependent Molecular Docking Process for Docking Small Flexible Molecules into Rigid Protein Receptors. 1638-1655
• 
  Shuangye Yin, Lada Biedermannová, Jirí Vondrásek, Nikolay V. Dokholyan:
  MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening. 1656-1662
• 
  Kirk Simmons, John Kinney, Aaron Owens, Daniel A. Kleier, Karen Bloch, Dave Argentar, Alicia Walsh, Ganesh Vaidyanathan:
  Comparative Study of Machine-Learning and Chemometric Tools for Analysis of In-Vivo High-Throughput Screening Data. 1663-1668

Computational Biochemistry

• 
  Daniele Casciari, Daniele Dell'Orco, Francesca Fanelli:
  Homodimerization of Neurotensin 1 Receptor Involves Helices 1, 2, and 4: Insights from Quaternary Structure Predictions and Dimerization Free Energy Estimations. 1669-1678
• 
  Shinji Soga, Hiroki Shirai, Masato Kobori, Noriaki Hirayama:
  Chemocavity: Specific Concavity in Protein Reserved for the Binding of Biologically Functional Small Molecules. 1679-1685

Pharmaceutical Modeling

• 
  Andrea Rizzi, Alessandro Fioni:
  Virtual Screening Using PLS Discriminant Analysis and ROC Curve Approach: An Application Study on PDE4 Inhibitors. 1686-1692
• 
  Patrick Markt, Caroline McGoohan, Brian Walker, Johannes Kirchmair, Clemens Feldmann, Gabriella De Martino, Gudrun M. Spitzer, Simona Distinto, Daniela Schuster, Gerhard Wolber, Christian Laggner, Thierry Langer:
  Discovery of Novel Cathepsin S Inhibitors by Pharmacophore-Based Virtual High-Throughput Screening. 1693-1705
• 
  Monique Araújo de Brito, Carlos Rangel Rodrigues, José Jair Vianna Cirino, Ricardo B. de Alencastro, Helena Castro, Magaly G. Albuquerque:
  3D-QSAR CoMFA of a Series of DABO Derivatives as HIV-1 Reverse Transcriptase Non-Nucleoside Inhibitors. 1706-1715
• 
  Rajarshi Guha, John H. Van Drie:
  Assessing How Well a Modeling Protocol Captures a Structure-Activity Landscape. 1716-1728

Book Reviews

• 
  Robert E. Buntrock:
  Book Review of Molecules and Medicine. 1729
• 
  Stephen R. Heller:
  Book Review of Google Version 2.0 - The Calculating Predator. 1729-1730
• 
  Robert E. Buntrock:
  Book Review of Innovate Like Edison: The Success System of America's Greatest Inventor. 1730
• 
  Stephen R. Heller:
  Book Review of The Adobe Illustrator CS Wow! Book (WOW!). 1730
• 
  Stephen R. Heller:
  Book Review of Apple Pro Training Series: Motion 3. 1730-1731

Volume 48, Number 9, September 2008

Chemical Information

• 
  Igor V. Tetko, Iurii Sushko, Anil Kumar Pandey, Hao Zhu, Alexander Tropsha, Ester Papa, Tomas Öberg, Roberto Todeschini, Denis Fourches, Alexandre Varnek:
  Critical Assessment of QSAR Models of Environmental Toxicity against Tetrahymena pyriformis: Focusing on Applicability Domain and Overfitting by Variable Selection. 1733-1746
• 
  Jens Auer, Jürgen Bajorath:
  Distinguishing between Bioactive and Modeled Compound Conformations through Mining of Emerging Chemical Patterns. 1747-1753
• 
  Yuan Wang, Jürgen Bajorath:
  Bit Silencing in Fingerprints Enables the Derivation of Compound Class-Directed Similarity Metrics. 1754-1759

Computational Chemistry

• 
  Mohamed Diwan M. AbdulHameed, Adel Hamza, Junjun Liu, Chang-Guo Zhan:
  Combined 3D-QSAR Modeling and Molecular Docking Study on Indolinone Derivatives as Inhibitors of 3-Phosphoinositide-Dependent Protein Kinase-1. 1760-1772
• 
  I-Jen Chen, Nicolas Foloppe:
  Conformational Sampling of Druglike Molecules with MOE and Catalyst: Implications for Pharmacophore Modeling and Virtual Screening. 1773-1791
• 
  Antonio Macchiarulo, Antimo Gioiello, Charles Thomas, Alberto Massarotti, Roberto Nuti, Emiliano Rosatelli, Paola Sabbatini, Kristina Schoonjans, Johan Auwerx, Roberto Pellicciari:
  Molecular Field Analysis and 3D-Quantitative Structure-Activity Relationship Study (MFA 3D-QSAR) Unveil Novel Features of Bile Acid Recognition at TGR5. 1792-1801

Computational Biochemistry

• 
  Qingye Zhang, Jiaoyan Yang, Kun Liang, Lingling Feng, Sanpin Li, Jian Wan, Xin Xu, Guangfu Yang, Deli Liu, Shao Yang:
  Binding Interaction Analysis of the Active Site and Its Inhibitors for Neuraminidase (N1 Subtype) of Human Influenza Virus by the Integration of Molecular Docking, FMO Calculation and 3D-QSAR CoMFA Modeling. 1802-1812

Pharmaceutical Modeling

• 
  Albert Duran, Guillermo C. Martínez, Manuel Pastor:
  Development and Validation of AMANDA, a New Algorithm for Selecting Highly Relevant Regions in Molecular Interaction Fields. 1813-1823
• 
  Jonathan Y. Mane, Mariusz Klobukowski, J. Torin Huzil, Jack Adam Tuszynski:
  Free Energy Calculations on the Binding of Colchicine and Its Derivatives with the α/β-Tubulin Isoforms. 1824-1832
• 
  James J. Langham, Ajay N. Jain:
  Accurate and Interpretable Computational Modeling of Chemical Mutagenicity. 1833-1839
• 
  Aleksejs Kontijevskis, Jan Komorowski, Jarl E. S. Wikberg:
  Generalized Proteochemometric Model of Multiple Cytochrome P450 Enzymes and Their Inhibitors. 1840-1850
• 
  Simone Sciabola, Robert V. Stanton, Sarah Wittkopp, Scott A. Wildman, Deborah J. Moshinsky, Shobha Potluri, Hualin Xi:
  Predicting Kinase Selectivity Profiles Using Free-Wilson QSAR Analysis. 1851-1867
• 
  Johannes Mohr, Brijnesh J. Jain, Klaus Obermayer:
  Molecule Kernels: A Descriptor- and Alignment-Free Quantitative Structure-Activity Relationship Approach. 1868-1881
• 
  Annu A. Soderholm, Johanna Viiliainen, Pekka T. Lehtovuori, Hanna Eskelinen, Daniela Röll, Aria Baniahmad, Tommi H. Nyrönen:
  Computationally Identified Novel Diphenyl- and Phenylpyridine Androgen Receptor Antagonist Structures. 1882-1890
• 
  Pramod C. Nair, Masilamani Elizabeth Sobhia:
  Fingerprint Directed Scaffold Hopping for Identification of CCR2 Antagonists. 1891-1902

Bioinformatics

• 
  Olav Zimmermann, Ulrich H. E. Hansmann:
  LOCUSTRA: Accurate Prediction of Local Protein Structure Using a Two-Layer Support Vector Machine Approach. 1903-1908

Software Description

• 
  S. Kashif Sadiq, David W. Wright, Simon J. Watson, Stefan J. Zasada, Ileana Stoica, Peter V. Coveney:
  Automated Molecular Simulation Based Binding Affinity Calculator for Ligand-Bound HIV-1 Proteases. 1909-1919
• 
  Benjamin T. Miller, Rishi P. Singh, Jeffery B. Klauda, Milan Hodoscek, Bernard R. Brooks, H. Lee Woodcock III:
  CHARMMing: A New, Flexible Web Portal for CHARMM. 1920-1929

Book Reviews

• 
  Stephen R. Heller:
  Book Review of Inspired CSS: Styling for a Beautiful Web (Video). 1930

Volume 48, Number 10, October 2008

Chemical Information

• 
  Vladimir J. Sykora, David E. Leahy:
  Chemical Descriptors Library (CDL): A Generic, Open Source Software Library for Chemical Informatics. 1931-1942
• 
  Laavanya Parthasarathi, Fergal P. Casey, Amelie Stein, Patrick Aloy, Denis C. Shields:
  Approved Drug Mimics of Short Peptide Ligands from Protein Interaction Motifs. 1943-1948
• 
  Paolo Mazzatorta, Manuel Dominguez Estevez, Myriam Coulet, Benoît Schilter:
  Modeling Oral Rat Chronic Toxicity. 1949-1954
• 
  Thomas J. Crisman, Mihiret Tekeste Sisay, Jürgen Bajorath:
  Ligand-Target Interaction-Based Weighting of Substructures for Virtual Screening. 1955-1964

Computational Chemistry

• 
  Jurgen Koska, Velin Z. Spassov, Allister J. Maynard, Lisa Yan, Nic Austin, Paul K. Flook, C. M. Venkatachalam:
  Fully Automated Molecular Mechanics Based Induced Fit Protein-Ligand Docking Method. 1965-1973
• 
  Julien Burton, Nathalie Meurice, Laurence Leherte, Daniel P. Vercauteren:
  Can Descriptors of the Electron Density Distribution Help To Distinguish Functional Groups? 1974-1983
• 
  Svetlana Markovic, Sonja Stankovic, Slavko Radenkovic, Ivan Gutman:
  Electronic Structure Study of Thermal Intraconversions of Some Dicyclopenta-Fused Polycyclic Aromatic Compounds. 1984-1989

Computational Biochemistry

• 
  Mahesh Kulharia, Roger S. Goody, Richard M. Jackson:
  Information Theory-Based Scoring Function for the Structure-Based Prediction of Protein-Ligand Binding Affinity. 1990-1998
• 
  Antonio Macchiarulo, Nicola Giacche, Andrea Carotti, Massimo Baroni, Gabriele Cruciani, Roberto Pellicciari:
  Targeting the Conformational Transitions of MDM2 and MDMX: Insights into Dissimilarities and Similarities of p53 Recognition. 1999-2009
• 
  Wei Deng, Christophe L. M. J. Verlinde:
  Evaluation of Different Virtual Screening Programs for Docking in a Charged Binding Pocket. 2010-2020
• 
  Ana Damjanovic, Benjamin T. Miller, Torre J. Wenaus, Petar Maksimovic, Bertrand García-Moreno E., Bernard R. Brooks:
  Open Science Grid Study of the Coupling between Conformation and Water Content in the Interior of a Protein. 2021-2029

Pharmaceutical Modeling

• 
  Lei Fang, Huai Zhang, Wei Cui, Mingjun Ji:
  Studies of the Mechanism of Selectivity of Protein Tyrosine Phosphatase 1B (PTP1B) Bidentate Inhibitors Using Molecular Dynamics Simulations and Free Energy Calculations. 2030-2041
• 
  Adam C. Lee, Jing-yu Yu, Gordon M. Crippen:
  pK_a Prediction of Monoprotic Small Molecules the SMARTS Way. 2042-2053
• 
  Osvaldo Andrade Santos-Filho, Artem Cherkasov:
  Using Molecular Docking, 3D-QSAR, and Cluster Analysis for Screening Structurally Diverse Data Sets of Pharmacological Interest. 2054-2065
• 
  John H. Streiff, Keith A. Jones:
  Volatile Anesthetic Binding to Proteins Is Influenced by Solvent and Aliphatic Residues. 2066-2073
• 
  Alfonso T. García-Sosa, Sulev Sild, Uko Maran:
  Design of Multi-Binding-Site Inhibitors, Ligand Efficiency, and Consensus Screening of Avian Influenza H5N1 Wild-Type Neuraminidase and of the Oseltamivir-Resistant H274Y Variant. 2074-2080

Bioinformatics

• 
  Dmitry A. Konovalov, Lyndon E. Llewellyn, Yvan Vander Heyden, Danny Coomans:
  Robust Cross-Validation of Linear Regression QSAR Models. 2081-2094

Book Reviews

• 
  Noel M. O'Boyle:
  Book Review of Gnuplot in Action. 2095

Volume 48, Number 11, November 2008

Chemical Information

• 
  Alexander Böcker:
  Toward an Improved Clustering of Large Data Sets Using Maximum Common Substructures and Topological Fingerprints. 2097-2107
• 
  Timothy J. Cheeseright, Mark D. Mackey, James L. Melville, Jeremy G. Vinter:
  FieldScreen: Virtual Screening Using Molecular Fields. Application to the DUD Data Set. 2108-2117
• 
  Nico Adams, Jerry Winter, Peter Murray-Rust, Henry S. Rzepa:
  Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language. 2118-2128
• 
  Eleonora Gianti, Luca Sartori:
  Identification and Selection of "Privileged Fragments" Suitable for Primary Screening. 2129-2139
• 
  Gerrit Schüürmann, Ralf-Uwe Ebert, Jingwen Chen, Bin Wang, Ralph Kühne:
  External Validation and Prediction Employing the Predictive Squared Correlation Coefficient Test Set Activity Mean vs Training Set Activity Mean. 2140-2145
• 
  Violeta I. Pérez-Nueno, David W. Ritchie, José I. Borrell, Jordi Teixidó:
  Clustering and Classifying Diverse HIV Entry Inhibitors Using a Novel Consensus Shape-Based Virtual Screening Approach: Further Evidence for Multiple Binding Sites within the CCR5 Extracellular Pocket. 2146-2165

Computational Chemistry

• 
  Cristina Tintori, Valentina Corradi, Matteo Magnani, Fabrizio Manetti, Maurizio Botta:
  Targets Looking for Drugs: A Multistep Computational Protocol for the Development of Structure-Based Pharmacophores and Their Applications for Hit Discovery. 2166-2179
• 
  Richard D. Cramer, Phillip Cruz, Gunther Stahl, William C. Curtiss, Brian Campbell, Brian B. Masek, Farhad Soltanshahi:
  Virtual Screening for R-Groups, including Predicted pIC50 Contributions, within Large Structural Databases, Using Topomer CoMFA. 2180-2195
• 
  Kirk Simmons, John Kinney, Aaron Owens, Daniel A. Kleier, Karen Bloch, Dave Argentar, Alicia Walsh, Ganesh Vaidyanathan:
  Practical Outcomes of Applying Ensemble Machine Learning Classifiers to High-Throughput Screening (HTS) Data Analysis and Screening. 2196-2206
• 
  Alan R. Katritzky, Dimitar A. Dobchev, Svetoslav H. Slavov, Mati Karelson:
  Legitimate Utilization of Large Descriptor Pools for QSPR/QSAR Models. 2207-2213
• 
  Marcel L. Verdonk, Paul N. Mortenson, Richard J. Hall, Michael J. Hartshorn, Christopher W. Murray:
  Protein-Ligand Docking against Non-Native Protein Conformers. 2214-2225
• 
  Hiroshi Takeuchi:
  Development of an Efficient Geometry Optimization Method for Water Clusters. 2226-2233

Computational Biochemistry

• 
  Jan Adam, Zdenek Kríz, Martin Prokop, Michaela Wimmerová, Jaroslav Koca:
  In Silico Mutagenesis and Docking Studies of Pseudomonas aeruginosa PA-IIL Lectin Predicting Binding Modes and Energies. 2234-2242

Pharmaceutical Modeling

• 
  Lívia Barros Salum, Igor Polikarpov, Adriano D. Andricopulo:
  Structure-Based Approach for the Study of Estrogen Receptor Binding Affinity and Subtype Selectivity. 2243-2253
• 
  Agnes Kapou, Nikolas-P. Benetis, Serdar Durdagi, Sotiris Nikolaropoulos, Thomas M. Mavromoustakos:
  3D QSAR/CoMFA and CoMSIA Studies on Antileukemic Steroidal Esters Coupled with Conformationally Flexible Nitrogen Mustards. 2254-2264

Bioinformatics

• 
  Guillermín Agüero-Chapín, Agostinho Antunes, Florencio M. Ubeira, Kuo-Chen Chou, Humberto González Díaz:
  Comparative Study of Topological Indices of Macro/Supramolecular RNA Complex Networks. 2265-2277
• 
  Helena Strömbergsson, Pawel Daniluk, Andriy Kryshtafovych, Krzysztof Fidelis, Jarl E. S. Wikberg, Gerard J. Kleywegt, Torgeir R. Hvidsten:
  Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space. 2278-2288

Volume 48, Number 12, December 2008

Letter

• 
  Francesco Colizzi, Maurizio Recanatini, Andrea Cavalli:
  Mechanical Features of Plasmodium falciparum Acyl Carrier Protein in the Delivery of Substrates. 2289-2293

Chemical Information

• 
  R. Webster Homer, Jon Swanson, Robert J. Jilek, Tad Hurst, Robert D. Clark:
  SYBYL Line Notation (SLN): A Single Notation To Represent Chemical Structures, Queries, Reactions, and Virtual Libraries. 2294-2307
• 
  Lu Tan, Eugen Lounkine, Jürgen Bajorath:
  Similarity Searching Using Fingerprints of Molecular Fragments Involved in Protein-Ligand Interactions. 2308-2312

Computational Chemistry

• 
  Florian Nigsch, Andreas Bender, Jeremy L. Jenkins, John B. O. Mitchell:
  Ligand-Target Prediction Using Winnow and Naive Bayesian Algorithms and the Implications of Overall Performance Statistics. 2313-2325
• 
  Peter C. Fox, Philippa R. N. Wolohan, Edmond J. Abrahamian, Robert D. Clark:
  Parameterization and Conformational Sampling Effects in Pharmacophore Multiplet Searching. 2326-2334

Computational Biochemistry

• 
  Masaaki Kotera, Andrew G. McDonald, Sinéad Boyce, Keith F. Tipton:
  Eliciting Possible Reaction Equations and Metabolic Pathways Involving Orphan Metabolites. 2335-2349
• 
  Nathalie Evrard-Todeschi, Julien Pons, Josyane Gharbi-Benarous, Gildas Bertho, Richard Benarous, Jean-Pierre Girault:
  Structure of the Complex between Phosphorylated Substrates and the SCF β-TrCP Ubiquitin Ligase Receptor: A Combined NMR, Molecular Modeling, and Docking Approach. 2350-2361

Pharmaceutical Modeling

• 
  Philip Prathipati, Ngai Ling Ma, Thomas H. Keller:
  Global Bayesian Models for the Prioritization of Antitubercular Agents. 2362-2370
• 
  Oleg V. Stroganov, Fedor N. Novikov, Viktor S. Stroylov, Val Kulkov, Ghermes G. Chilov:
  Lead Finder: An Approach To Improve Accuracy of Protein-Ligand Docking, Binding Energy Estimation, and Virtual Screening. 2371-2385
• 
  Ravi Nandigam, David A. Evans, Jon A. Erickson, Sangtae Kim, Jeffrey J. Sutherland:
  Predicting the Accuracy of Ligand Overlay Methods with Random Forest Models. 2386-2394
• 
  Felix Deanda, Eugene L. Stewart, Michael J. Reno, David H. Drewry:
  Kinase-Targeted Library Design through the Application of the PharmPrint Methodology. 2395-2403

Software Description

• 
  Jan H. Jensen, Thomas Hoeg-Jensen, Søren B. Padkjær:
  Building a BioChemformatics Database. 2404-2413
• 
  Toon Verstraelen, Marc Van Houteghem, Veronique Van Speybroeck, Michel Waroquier:
  MD-TRACKS: A Productive Solution for the Advanced Analysis of Molecular Dynamics and Monte Carlo simulations. 2414-2424