Journal of Chemical Information and Modeling, Volume 50

Volume 50, Number 1, January 2010

Chemical Information

• 
  J. Robert Fischer, Uta F. Lessel, Matthias Rarey:
  LoFT: Similarity-Driven Multiobjective Focused Library Design. 1-21
• 
  Jiang Li, Peter Willett:
  Bibliometric Analysis of Chinese Research on Cyclization, MALDI-TOF, and Antibiotics. 22-29
• 
  Stefan Rannar, Patrik L. Andersson:
  A Novel Approach Using Hierarchical Clustering To Select Industrial Chemicals for Environmental Impact Assessment. 30-36
• 
  Alex M. Clark:
  2D Depiction of Fragment Hierarchies. 37-46
• 
  Yingyao Zhou, Bin Zhou, Shumei Jiang, Frederick J. King:
  Chemical-Text Hybrid Search Engines. 47-54
• 
  Junmei Wang, Tingjun Hou:
  Drug and Drug Candidate Building Block Analysis. 55-67
• 
  Eugen Lounkine, Mathias Wawer, Anne Mai Wassermann, Jürgen Bajorath:
  SARANEA: A Freely Available Program To Mine Structure-Activity and Structure-Selectivity Relationship Information in Compound Data Sets. 68-78
• 
  José Batista, Lu Tan, Jürgen Bajorath:
  Atom-Centered Interacting Fragments and Similarity Search Applications. 79-86

Computational Chemistry

• 
  Glenn I. Hawe, Ibon Alkorta, Paul L. A. Popelier:
  Prediction of the Basicities of Pyridines in the Gas Phase and in Aqueous Solution. 87-96
• 
  Renato F. Freitas, Renato de Lima Bauab, Carlos Alberto Montanari:
  Novel Application of 2D and 3D-Similarity Searches To Identify Substrates among Cytochrome P450 2C9, 2D6, and 3A4. 97-109

Computational Biochemistry

• 
  Jans H. Alzate-Morales, Julio Caballero:
  Computational Study of the Interactions between Guanine Derivatives and Cyclin-Dependent Kinase 2 (CDK2) by CoMFA and QM/MM. 110-122
• 
  Nathanael Weill, Didier Rognan:
  Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein-Ligand Binding Sites. 123-135

Pharmaceutical Modeling

• 
  Ming Han, John Z. H. Zhang:
  Class I Phospho-inositide-3-kinases (PI3Ks) Isoform-Specific Inhibition Study by the Combination of Docking and Molecular Dynamics Simulation. 136-145
• 
  Rita Santos, Jozef Hritz, Chris Oostenbrink:
  Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6. 146-154
• 
  Simone Sciabola, Robert V. Stanton, James E. J. Mills, Maria M. Flocco, Massimo Baroni, Gabriele Cruciani, Francesca Perruccio, Jonathan S. Mason:
  High-Throughput Virtual Screening of Proteins Using GRID Molecular Interaction Fields. 155-169
• 
  Tomohiro Sato, Teruki Honma, Shigeyuki Yokoyama:
  Combining Machine Learning and Pharmacophore-Based Interaction Fingerprint for in Silico Screening. 170-185
• 
  Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan:
  Recipes for the Selection of Experimental Protein Conformations for Virtual Screening. 186-193
• 
  Suman Sirimulla, Maricarmen Lerma, William C. Herndon:
  Prediction of Partial Molar Volumes of Amino Acids and Small Peptides: Counting Atoms versus Topological Indices. 194-204

Volume 50, Number 2, February 2010

Perspective

• 
  Hanna Geppert, Martin Vogt, Jürgen Bajorath:
  Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation. 205-216

Letter

• 
  Michael Seitz, Nicola Alzakhem:
  Computational Estimation of Lanthanoid-Water Bond Lengths by Semiempirical Methods. 217-220

Chemical Information

• 
  Frédéric Pennerath, Gilles Niel, Philippe Vismara, Philippe Jauffret, Claude Laurenço, Amedeo Napoli:
  Graph-Mining Algorithm for the Evaluation of Bond Formability. 221-239
• 
  Xialan Dong, Jerry Osagie Ebalunode, Sung Jin Cho, Weifan Zheng:
  A Novel Structure-Based Multimode QSAR Method Affords Predictive Models for Phosphodiesterase Inhibitors. 240-250
• 
  Jim Downing, Matt J. Harvey, Peter B. Morgan, Peter Murray-Rust, Henry S. Rzepa, Diana C. Stewart, Alan P. Tonge, Joe Townsend:
  SPECTRa-T: Machine-Based Data Extraction and Semantic Searching of Chemistry e-Theses. 251-261

Computational Chemistry

• 
  Sheng-You Huang, Xiaoqin Zou:
  Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein-Ligand Interactions. 262-273
• 
  Jörg Bentzien, Eugene R. Hickey, Raymond A. Kemper, Mark L. Brewer, Jane D. Dyekjær, Stephen P. East, Mark Whittaker:
  An in Silico Method for Predicting Ames Activities of Primary Aromatic Amines by Calculating the Stabilities of Nitrenium Ions. 274-297
• 
  Sourav Das, Michael P. Krein, Curt M. Breneman:
  Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures. 298-308

Pharmaceutical Modeling

• 
  Mark Vere Culp, Kjell Johnson, George Michailidis:
  The Ensemble Bridge Algorithm: A New Modeling Tool for Drug Discovery Problems. 309-316
• 
  Qingye Zhang, Ding Li, Pei Wei, Jie Zhang, Jian Wan, Yangliang Ren, Zhigang Chen, Deli Liu, Ziniu Yu, Lingling Feng:
  Structure-Based Rational Screening of Novel Hit Compounds with Structural Diversity for Cytochrome P450 Sterol 14α-Demethylase from Penicillium digitatum. 317-325

Book Reviews

• 
  Milan Randic:
  Book Review of Molecular Descriptors for Chemoinformatics - Second, Revised and Enlarged Edition (Volume I: Alphabetical Listing; Volume II: Appendices, Bibliography). 326

Volume 50, Number 3, March 2010

Chemical Information

• 
  Akio Tanaka, Hideho Okamoto, Malcolm Bersohn:
  Construction of Functional Group Reactivity Database under Various Reaction Conditions Automatically Extracted from Reaction Database in a Synthesis Design System. 327-338
• 
  Jameed Hussain, Ceara Rea:
  Computationally Efficient Algorithm to Identify Matched Molecular Pairs (MMPs) in Large Data Sets. 339-348

Computational Chemistry

• 
  Michael Devereux, Markus Meuwly:
  Force Field Optimization using Dynamics and Ensemble Averaged Data: Vibrational Spectra and Relaxation in Bound MbCO. 349-357
• 
  Valérie Campagna-Slater, Andrew G. Arrowsmith, Yong Zhao, Matthieu Schapira:
  Pharmacophore Screening of the Protein Data Bank for Specific Binding Site Chemistry. 358-367

Computational Biochemistry

• 
  Slimane Doudou, Raman Sharma, Richard H. Henchman, David W. Sheppard, Neil A. Burton:
  Inhibitors of PIM-1 Kinase: A Computational Analysis of the Binding Free Energies of a Range of Imidazo [1, 2-b] Pyridazines. 368-379
• 
  Wei Cui, Zhuo Wei, Quan Chen, Yuanhua Cheng, Lingling Geng, Jian Zhang, Jianhua Chen, Tingjun Hou, Mingjuan Ji:
  Structure-Based Design of Peptides against G3BP with Cytotoxicity on Tumor Cells. 380-387
• 
  Nikolaos Dimitropoulos, Athanasios Papakyriakou, Georgios A. Dalkas, Edward D. Sturrock, Georgios Spyroulias:
  A Computational Approach to the Study of the Binding Mode of Dual ACE/NEP Inhibitors. 388-396
• 
  Ignasi Buch, Matt J. Harvey, Toni Giorgino, David P. Anderson, Gianni De Fabritiis:
  High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing. 397-403

Pharmaceutical Modeling

• 
  Christian Kramer, Bernd Beck, Timothy Clark:
  Insolubility Classification with Accurate Prediction Probabilities Using a MetaClassifier. 404-414
• 
  Ramasamy Thilagavathi, Ricardo L. Mancera:
  Ligand-Protein Cross-Docking with Water Molecules. 415-421
• 
  Jana Sopkova-de Oliveira Santos, Aurélien Lesnard, Jean-Hugues Agondanou, Nathalie Dupont, Anne-Marie Godard, Silvia Stiebing, Christophe Rochais, Frédéric Fabis, Patrick Dallemagne, Ronan Bureau, Sylvain Rault:
  Virtual Screening Discovery of New Acetylcholinesterase Inhibitors Issued from CERMN Chemical Library. 422-428
• 
  Christian Kramer, Bernd Beck, Timothy Clark:
  A Surface-Integral Model for Log P_OW. 429-436
• 
  Anwar Rayan, David Marcus, Amiram Goldblum:
  Predicting Oral Druglikeness by Iterative Stochastic Elimination. 437-445
• 
  Alban Lepailleur, Stéphane Lemaître, Xiao Feng, Jana Sopkova-de Oliveira Santos, Philippe Delagrange, Jean Boutin, Pierre Renard, Ronan Bureau, Sylvain Rault:
  Receptor- and Ligand-Based Study on Novel 2, 2′-Bithienyl Derivatives as Non-Peptidic AANAT Inhibitors. 446-460

Volume 50, Number 4, April 2010

Chemical Information

• 
  Kevin Theisen, Berend Smit, Maciej Haranczyk:
  Chemical Hieroglyphs: Abstract Depiction of Complex Void Space Topology of Nanoporous Materials. 461-469
• 
  Alexander Chuprina, Oleg Lukin, Robert Demoiseaux, Alexander Buzko, Alexander Shivanyuk:
  Drug- and Lead-likeness, Target Class, and Molecular Diversity Analysis of 7.9 Million Commercially Available Organic Compounds Provided by 29 Suppliers. 470-479
• 
  Sara Núñez, Jennifer Venhorst, Chris G. Kruse:
  Assessment of a Novel Scoring Method Based on Solvent Accessible Surface Area Descriptors. 480-486
• 
  Hany E. A. Ahmed, Martin Vogt, Jürgen Bajorath:
  Design and Evaluation of Bonded Atom Pair Descriptors. 487-499
• 
  Ye Hu, Jürgen Bajorath:
  Molecular Scaffolds with High Propensity to Form Multi-Target Activity Cliffs. 500-510

Computational Chemistry

• 
  Ian R. Craig, Jonathan W. Essex, Katrin Spiegel:
  Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments. 511-524
• 
  Jason G. Kettle, Richard A. Ward:
  Toward the Comprehensive Systematic Enumeration and Synthesis of Novel Kinase Inhibitors Based on a 4-Anilinoquinazoline Binding Mode. 525-533
• 
  K. Shawn Watts, Pranav Dalal, Robert B. Murphy, Woody Sherman, Richard A. Friesner, John C. Shelley:
  ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers. 534-546
• 
  Cristiano Ruch Werneck Guimarães, Alan M. Mathiowetz:
  Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations. 547-559
• 
  Imran S. Haque, Vijay S. Pande, W. Patrick Walters:
  SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs. 560-564
• 
  John Manchester, Grant Walkup, Olga Rivin, Zhiping You:
  Evaluation of pK_a Estimation Methods on 211 Druglike Compounds. 565-571
• 
  Paul C. D. Hawkins, A. Geoffrey Skillman, Gregory L. Warren, Benjamin A. Ellingson, Matthew T. Stahl:
  Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database. 572-584
• 
  Anitha Ramraj, Ian H. Hillier:
  Binding of Pollutant Aromatics on Carbon Nanotubes and Graphite. 585-588

Computational Biochemistry

• 
  Ryan G. Coleman, Kim A. Sharp:
  Protein Pockets: Inventory, Shape, and Comparison. 589-603
• 
  Martin Sippel, Christoph A. Sotriffer:
  Molecular Dynamics Simulations of the HIV-1 Integrase Dimerization Interface: Guidelines for the Design of a Novel Class of Integrase Inhibitors. 604-614
• 
  Zhi Chen, Guanghui Tian, Zhen Wang, Hualiang Jiang, Jingshan Shen, Weiliang Zhu:
  Multiple Pharmacophore Models Combined with Molecular Docking: A Reliable Way for Efficiently Identifying Novel PDE4 Inhibitors with High Structural Diversity. 615-625
• 
  Fiona M. McRobb, Ben Capuano, Ian T. Crosby, David K. Chalmers, Elizabeth Yuriev:
  Homology Modeling and Docking Evaluation of Aminergic G Protein-Coupled Receptors. 626-637
• 
  Mattia Mori, Ursula Dietrich, Fabrizio Manetti, Maurizio Botta:
  Molecular Dynamics and DFT Study on HIV-1 Nucleocapsid Protein-7 in Complex with Viral Genome. 638-650

Pharmaceutical Modeling

• 
  Xiaohua Zhang, Alan C. Gibbs, Charles H. Reynolds, Martin B. Peters, Lance M. Westerhoff:
  Quantum Mechanical Pairwise Decomposition Analysis of Protein Kinase B Inhibitors: Validating a New Tool for Guiding Drug Design. 651-661
• 
  Ira Musmuca, Antonia Caroli, Antonello Mai, Neerja Kaushik-Basu, Payal Arora, Rino Ragno:
  Combining 3-D Quantitative Structure-Activity Relationship with Ligand Based and Structure Based Alignment Procedures for in Silico Screening of New Hepatitis C Virus NS5B Polymerase Inhibitors. 662-676
• 
  Ernst Ahlberg Helgee, Lars Carlsson, Scott Boyer, Ulf Norinder:
  Evaluation of Quantitative Structure-Activity Relationship Modeling Strategies: Local and Global Models. 677-689

Bioinformatics

• 
  Joji M. Otaki, Motosuke Tsutsumi, Tomonori Gotoh, Haruhiko Yamamoto:
  Secondary Structure Characterization Based on Amino Acid Composition and Availability in Proteins. 690-700

Volume 50, Number 5, May 2010

Chemical Information

• 
  Leo Ghemtio, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Michel Souchet, Vincent Leroux, Bernard Maigret:
  Comparison of Three Preprocessing Filters Efficiency in Virtual Screening: Identification of New Putative LXRβ Regulators As a Test Case. 701-715
• 
  Shivani Agarwal, Deepak Dugar, Shiladitya Sengupta:
  Ranking Chemical Structures for Drug Discovery: A New Machine Learning Approach. 716-731
• 
  Joo-Young Choi, Melissa J. Davis, Andrew F. Newman, Mark A. Ragan:
  A Semantic Web Ontology for Small Molecules and Their Biological Targets. 732-741
• 
  David Rogers, Mathew Hahn:
  Extended-Connectivity Fingerprints. 742-754
• 
  Punnaivanam Sankar, Alain Krief, Gnanasekaran Aghila:
  Model Tool to Describe Chemical Structures in XML Format Utilizing Structural Fragments and Chemical Ontology. 755-770
• 
  G. Madhavi Sastry, Jeffrey F. Lowrie, Steven L. Dixon, Woody Sherman:
  Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments. 771-784
• 
  Ghanima Al-Sharrah:
  Ranking Using the Copeland Score: A Comparison with the Hasse Diagram. 785-791

Computational Chemistry

• 
  Paul Labute:
  LowModeMD - Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops. 792-800
• 
  Miriam López-Ramos, Francesca Perruccio:
  HPPD: Ligand- and Target-Based Virtual Screening on a Herbicide Target. 801-814
• 
  Kazuki Ohno, Yuichi Nagahara, Kazuhisa Tsunoyama, Masaya Orita:
  Are There Differences between Launched Drugs, Clinical Candidates, and Commercially Available Compounds? 815-821
• 
  I-Jen Chen, Nicolas Foloppe:
  Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst. 822-839
• 
  Sandhya Kortagere, William J. Welsh, Joanne M. Morrisey, Thomas Daly, Ijeoma Ejigiri, Photini Sinnis, Akhil B. Vaidya, Lawrence W. Bergman:
  Structure-based Design of Novel Small-Molecule Inhibitors of Plasmodium falciparum. 840-849
• 
  Tatsusada Yoshida, Yohei Munei, Seiji Hitaoka, Hiroshi Chuman:
  Correlation Analyses on Binding Affinity of Substituted Benzenesulfonamides with Carbonic Anhydrase Using ab Initio MO Calculations on Their Complex Structures. 850-860
• 
  Jiazhong Li, Paola Gramatica:
  Classification and Virtual Screening of Androgen Receptor Antagonists. 861-874

Computational Biochemistry

• 
  Ying Wang, Dongqing Wei, Jing-Fang Wang:
  Molecular Dynamics Studies on T1 Lipase: Insight into a Double-Flap Mechanism. 875-878
• 
  René Meier, Martin Pippel, Frank Brandt, Wolfgang Sippl, Carsten Baldauf:
  ParaDockS: A Framework for Molecular Docking with Population-Based Metaheuristics. 879-889
• 
  S. Kashif Sadiq, David W. Wright, Owain Kenway, Peter V. Coveney:
  Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases. 890-905

Pharmaceutical Modeling

• 
  Prasenjit Mukherjee, Prashant V. Desai, Yu-Dong Zhou, Mitchell A. Avery:
  Targeting the BH3 Domain Mediated Protein-Protein Interaction of Bcl-xL through Virtual Screening. 906-923

Bioinformatics

• 
  Alberto Rolo-Naranjo, Edelsys Codorniu-Hernández, Noel Ferro:
  Quantum Chemical Associations Ligand-Residue: Their Role to Predict Flavonoid Binding Sites in Proteins. 924-933
• 
  Yusuke Ishida, Yuki Kato, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu:
  Branch-and-Bound Algorithms for Enumerating Treelike Chemical Graphs with Given Path Frequency Using Detachment-Cut. 934-946
• 
  Jeremy Esque, Christophe Oguey, Alexandre G. de Brevern:
  A Novel Evaluation of Residue and Protein Volumes by Means of Laguerre Tessellation. 947-960

Volume 50, Number 6, June 2010

Perspective

• 
  Lisa Michielan, Stefano Moro:
  Pharmaceutical Perspectives of Nonlinear QSAR Strategies. 961-978

Chemical Information

• 
  Yevgeniy Podolyan, Michael A. Walters, George Karypis:
  Assessing Synthetic Accessibility of Chemical Compounds Using Machine Learning Methods. 979-991
• 
  David Giganti, Hélène Guillemain, Jean-Louis Spadoni, Michael Nilges, Jean-François Zagury, Matthieu Montès:
  Comparative Evaluation of 3D Virtual Ligand Screening Methods: Impact of the Molecular Alignment on Enrichment. 992-1004
• 
  Salla I. Virtanen, Olli T. Pentikäinen:
  Efficient Virtual Screening Using Multiple Protein Conformations Described as Negative Images of the Ligand-Binding Site. 1005-1011
• 
  Ammar Abdo, Beining Chen, Christoph Müller, Naomie Salim, Peter Willett:
  Ligand-Based Virtual Screening Using Bayesian Networks. 1012-1020
• 
  Lisa Peltason, Preeti Iyer, Jürgen Bajorath:
  Rationalizing Three-Dimensional Activity Landscapes and the Influence of Molecular Representations on Landscape Topology and the Formation of Activity Cliffs. 1021-1033
• 
  Jie Shen, Feixiong Cheng, You Xu, Weihua Li, Yun Tang:
  Estimation of ADME Properties with Substructure Pattern Recognition. 1034-1041
• 
  Lu Tan, José Batista, Jürgen Bajorath:
  Rationalization of the Performance and Target Dependence of Similarity Searching Incorporating Protein-Ligand Interaction Information. 1042-1052

Computational Chemistry

• 
  Olga Obrezanova, Matthew D. Segall:
  Gaussian Processes for Classification: QSAR Modeling of ADMET and Target Activity. 1053-1061
• 
  Francesca Milletti, Anna Vulpetti:
  Tautomer Preference in PDB Complexes and its Impact on Structure-Based Drug Discovery. 1062-1074
• 
  Imran S. Haque, Vijay S. Pande:
  SCISSORS: A Linear-Algebraical Technique to Rapidly Approximate Chemical Similarities. 1075-1088

Computational Biochemistry

• 
  Xiaoying Hu, Aixia Yan, Tianwei Tan, Oliver Sacher, Johann Gasteiger:
  Similarity Perception of Reactions Catalyzed by Oxidoreductases and Hydrolases Using Different Classification Methods. 1089-1100
• 
  Jans H. Alzate-Morales, Ariela Vergara Jaque, Julio Caballero:
  Computational Study on the Interaction of N1 Substituted Pyrazole Derivatives with B-Raf Kinase: An Unusual Water Wire Hydrogen-Bond Network and Novel Interactions at the Entrance of the Active Site. 1101-1112
• 
  Luciana Gavernet, Jose L. Gonzalez Funes, Luis Bruno Blanch, Guillermina Estiu, Alfonso Maresca, Claudiu T. Supuran:
  Affinity of Sulfamates and Sulfamides to Carbonic Anhydrase II Isoform: Experimental and Molecular Modeling Approaches. 1113-1122

Pharmaceutical Modeling

• 
  Kristi Yi Fan, Raymond J. Unwalla, Rajiah Aldrin Denny, Li Di, Edward H. Kerns, David J. Diller, Christine Humblet:
  Insights for Predicting Blood-Brain Barrier Penetration of CNS Targeted Molecules Using QSPR Approaches. 1123-1133
• 
  Yaozong Li, Jie Shen, Xianqiang Sun, Weihua Li, Guixia Liu, Yun Tang:
  Accuracy Assessment of Protein-Based Docking Programs against RNA Targets. 1134-1146
• 
  Rajendra Kumar, Ranajit Nivrutti Shinde, Dara Ajay, Masilamani Elizabeth Sobhia:
  Probing Interaction Requirements in PTP1B Inhibitors: A Comparative Molecular Dynamics Study. 1147-1158
• 
  Brett R. Beno, David R. Langley:
  MORPH: A New Tool for Ligand Design. 1159-1164
• 
  Mark Sandor, Robert Kiss, György M. Keserü:
  Virtual Fragment Docking by Glide: a Validation Study on 190 Protein-Fragment Complexes. 1165-1172
• 
  Toshimasa Itoh, Hitomi Takemura, Kayoko Shimoi, Keiko Yamamoto:
  A 3D Model of CYP1B1 Explains the Dominant 4-Hydroxylation of Estradiol. 1173-1178

Bioinformatics

• 
  Michael Fernández, Shandar Ahmad, Akinori Sarai:
  Proteochemometric Recognition of Stable Kinase Inhibition Complexes Using Topological Autocorrelation and Support Vector Machines. 1179-1188

Volume 50, Number 7, July 2010

Perspective

• 
  Denis Fourches, Eugene N. Muratov, Alexander Tropsha:
  Trust, But Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research. 1189-1204

Chemical Information

• 
  Pierre Baldi, Ramzi Nasr:
  When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values. 1205-1222
• 
  Torsten Thalheim, Armin Vollmer, Ralf-Uwe Ebert, Ralph Kühne, Gerrit Schüürmann:
  Tautomer Identification and Tautomer Structure Generation Based on the InChI Code. 1223-1232
• 
  Yoshifumi Fukunishi, Kazuki Ohno, Masaya Orita, Haruki Nakamura:
  Selection of In Silico Drug Screening Results by Using Universal Active Probes (UAPs). 1233-1240
• 
  Gudrun M. Spitzer, Mathias Heiss, Martina Mangold, Patrick Markt, Johannes Kirchmair, Gerhard Wolber, Klaus R. Liedl:
  One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space. 1241-1247
• 
  Anne Mai Wassermann, Jürgen Bajorath:
  Chemical Substitutions That Introduce Activity Cliffs Across Different Compound Classes and Biological Targets. 1248-1256

Computational Chemistry

• 
  David H. White, Richard C. Wilson:
  Generative Models for Chemical Structures. 1257-1274
• 
  Indrek Tulp, Dimitar A. Dobchev, Alan R. Katritzky, William E. Acree Jr., Uko Maran:
  A General Treatment of Solubility 4. Description and Analysis of a PCA Model for Ostwald Solubility Coefficients. 1275-1283
• 
  Melvin J. Yu:
  Predicting Total Clearance in Humans from Chemical Structure. 1284-1295

Pharmaceutical Modeling

• 
  James R. Damewood, Charles L. Lerman, Brian B. Masek:
  NovoFLAP: A Ligand-Based De Novo Design Approach for the Generation of Medicinally Relevant Ideas. 1296-1303
• 
  Bo-Han Su, Meng-yu Shen, Emilio Xavier Esposito, Anton J. Hopfinger, Yufeng J. Tseng:
  In Silico Binary Classification QSAR Models Based on 4D-Fingerprints and MOE Descriptors for Prediction of hERG Blockage. 1304-1318

Volume 50, Number 8, August 2010

Chemical Information

• 
  James B. Hendrickson:
  Systematic Signatures for Organic Reactions. 1319-1329
• 
  Sylvain Lozano, Guillaume Poezevara, Marie-Pierre Halm-Lemeille, Elodie Lescot-Fontaine, Alban Lepailleur, Ryan Bissell-Siders, Bruno Crémilleux, Sylvain Rault, Bertrand Cuissart, Ronan Bureau:
  Introduction of Jumping Fragments in Combination with QSARs for the Assessment of Classification in Ecotoxicology. 1330-1339
• 
  Shereena M. Arif, John D. Holliday, Peter Willett:
  Inverse Frequency Weighting of Fragments for Similarity-Based Virtual Screening. 1340-1349
• 
  Daniel J. Warner, Edward J. Griffen, Stephen A. St-Gallay:
  WizePairZ: A Novel Algorithm to Identify, Encode, and Exploit Matched Molecular Pairs with Unspecified Cores in Medicinal Chemistry. 1350-1357
• 
  Ramzi Nasr, Daniel S. Hirschberg, Pierre Baldi:
  Hashing Algorithms and Data Structures for Rapid Searches of Fingerprint Vectors. 1358-1368
• 
  Grazyna Nowak, Grzegorz Fic:
  Search for Complexity Generating Chemical Transformations by Combining Connectivity Analysis and Cascade Transformation Patterns. 1369-1377
• 
  Mengzhu Xue, Mingyue Zheng, Bing Xiong, Yanlian Li, Hualiang Jiang, Jingkang Shen:
  Knowledge-Based Scoring Functions in Drug Design. 1. Developing a Target-Specific Method for Kinase-Ligand Interactions. 1378-1386
• 
  Oleg Ursu, Tudor I. Oprea:
  Model-Free Drug-Likeness from Fragments. 1387-1394
• 
  Mathias Wawer, Jürgen Bajorath:
  Similarity-Potency Trees: A Method to Search for SAR Information in Compound Data Sets and Derive SAR Rules. 1395-1409

Computational Chemistry

• 
  Nadtanet Nunthaboot, Thanyada Rungrotmongkol, Maturos Malaisree, Nopporn Kaiyawet, Panita Decha, Pornthep Sompornpisut, Yong Poovorawan, Supot Hannongbua:
  Evolution of Human Receptor Binding Affinity of H1N1 Hemagglutinins from 1918 to 2009 Pandemic Influenza A Virus. 1410-1417
• 
  Francesca Milletti, Anna Vulpetti:
  Predicting Polypharmacology by Binding Site Similarity: From Kinases to the Protein Universe. 1418-1431
• 
  Tiziano Tuccinardi, Maurizio Botta, Antonio Giordano, Adriano Martinelli:
  Protein Kinases: Docking and Homology Modeling Reliability. 1432-1441
• 
  Simon Cross, Massimo Baroni, Emanuele Carosati, Paolo Benedetti, Sérgio Clementi:
  FLAP: GRID Molecular Interaction Fields in Virtual Screening. Validation using the DUD Data Set. 1442-1450
• 
  Cristina Dezi, Andrea Carotti, Matteo Magnani, Massimo Baroni, Alessandro Padova, Gabriele Cruciani, Antonio Macchiarulo, Roberto Pellicciari:
  Molecular Interaction Fields and 3D-QSAR Studies of p53-MDM2 Inhibitors Suggest Additional Features of Ligand-Target Interaction. 1451-1465
• 
  Howard J. Feldman, Paul Labute:
  Pocket Similarity: Are α Carbons Enough? 1466-1475

Computational Biochemistry

• 
  Peng Zhou, Feifei Tian, Yanrong Ren, Zhicai Shang:
  Systematic Classification and Analysis of Themes in Protein-DNA Recognition. 1476-1488
• 
  Simone Fulle, Nina Alexandra Christ, Eva Kestner, Holger Gohlke:
  HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations. 1489-1501

Pharmaceutical Modeling

• 
  Rama K. Mishra, Jasbir Singh:
  Generation, Validation, and Utilization of a Three-Dimensional Pharmacophore Model for EP3 Antagonists. 1502-1509
• 
  Amit K. Gupta, S. Chakroborty, Kumkum Srivastava, Sunil K. Puri, Anil K. Saxena:
  Pharmacophore Modeling of Substituted 1, 2, 4-Trioxanes for Quantitative Prediction of their Antimalarial Activity. 1510-1520

Volume 50, Number 9, September 2010

Letter

• 
  Roustem D. Saiakhov, Gilles Klopman:
  Benchmark Performance of MultiCASE Inc. Software in Ames Mutagenicity Set. 1521
• 
  Miriam Sgobba, Rosetta Forestiero, Gianluca Degliesposti, Giulio Rastelli:
  Exploring the Binding Site of C-Terminal Hsp90 Inhibitors. 1522-1528

Chemical Information

• 
  Karen Schomburg, Hans-Christian Ehrlich, Katrin Stierand, Matthias Rarey:
  From Structure Diagrams to Visual Chemical Patterns. 1529-1535
• 
  György G. Ferenczy, György M. Keserü:
  Enthalpic Efficiency of Ligand Binding. 1536-1541

Computational Chemistry

• 
  Andrew G. Mercader, Pablo Duchowicz, Francisco M. Fernández, Eduardo A. Castro:
  Replacement Method and Enhanced Replacement Method Versus the Genetic Algorithm Approach for the Selection of Molecular Descriptors in QSPR/QSAR Theories. 1542-1548
• 
  Miklos Feher, Christopher I. Williams:
  Reducing Docking Score Variations Arising from Input Differences. 1549-1560
• 
  Michael M. Mysinger, Brian K. Shoichet:
  Rapid Context-Dependent Ligand Desolvation in Molecular Docking. 1561-1573
• 
  Kanin Wichapong, Michael Lawson, Somsak Pianwanit, Sirirat Kokpol, Wolfgang Sippl:
  Postprocessing of Protein-Ligand Docking Poses Using Linear Response MM-PB/SA: Application to Wee1 Kinase Inhibitors. 1574-1588
• 
  Varnavas D. Mouchlis, Thomas M. Mavromoustakos, George Kokotos:
  Molecular Docking and 3D-QSAR CoMFA Studies on Indole Inhibitors of GIIA Secreted Phospholipase A₂. 1589-1601

Computational Biochemistry

• 
  Shu Cheng, Masha Y. Niv:
  Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation. 1602-1610
• 
  Catharine Collar, Moses Lee, W. David Wilson:
  Setting Anchor in the Minor Groove: in Silico Investigation into Formamido N-Methylpyrrole and N-Methylimidazole Polyamides Bound by Cognate DNA Sequences. 1611-1622
• 
  Feng Ding, Shuangye Yin, Nikolay V. Dokholyan:
  Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands. 1623-1632
• 
  Yaxue Zhao, Xuefeng Lu, Chao-Yie Yang, Zhimin Huang, Wei Fu, Tingjun Hou, Jian Zhang:
  Computational Modeling Toward Understanding Agonist Binding on Dopamine 3. 1633-1643

Pharmaceutical Modeling

• 
  Patrick Pfeffer, Thomas Fober, Eyke Hüllermeier, Gerhard Klebe:
  GARLig: A Fully Automated Tool for Subset Selection of Large Fragment Spaces via a Self-Adaptive Genetic Algorithm. 1644-1659
• 
  Kurt De Grave, Fabrizio Costa:
  Molecular Graph Augmentation with Rings and Functional Groups. 1660-1668
• 
  Oliver Korb, Peter Monecke, Gerhard Hessler, Thomas Stützle, Thomas E. Exner:
  pharmACOphore: Multiple Flexible Ligand Alignment Based on Ant Colony Optimization. 1669-1681
• 
  Yan Li, Zhihai Liu, Renxiao Wang:
  Test MM-PB/SA on True Conformational Ensembles of Protein-Ligand Complexes. 1682-1692
• 
  Matheus P. Postigo, Rafael V. C. Guido, Glaucius Oliva, Marcelo Santos Castilho, Ivan da R. Pitta, Julianna F. C. de Albuquerque, Adriano D. Andricopulo:
  Discovery of New Inhibitors of Schistosoma mansoni PNP by Pharmacophore-Based Virtual Screening. 1693-1705
• 
  Mahmoud A. Al-Sha'er, Mutasem O. Taha:
  Elaborate Ligand-Based Modeling Reveals New Nanomolar Heat Shock Protein 90α Inhibitors. 1706-1723
• 
  Shek Ling Chan, Paul Labute:
  Training a Scoring Function for the Alignment of Small Molecules. 1724-1735

Software Description

• 
  An Ghysels, Toon Verstraelen, Karen Hemelsoet, Michel Waroquier, Veronique Van Speybroeck:
  TAMkin: A Versatile Package for Vibrational Analysis and Chemical Kinetics. 1736-1750
• 
  John D. Crabtree, Dinesh P. Mehta, Tina M. Kouri:
  An Open-Source Java Platform for Automated Reaction Mapping. 1751-1756

Computer Software Reviews

• 
  Stephen R. Heller:
  Corel WordPerfect X5. 1757

Volume 50, Number 10, October 2010

Chemical Information

• 
  Gene M. Ko, A. Srinivas Reddy, Sunil Kumar, Barbara A. Bailey, Rajni Garg:
  Computational Analysis of HIV-1 Protease Protein Binding Pockets. 1759-1771
• 
  Albert J. Kooistra, Thomas W. Binsl, Johannes H. G. M. van Beek, Chris de Graaf, Jaap Heringa:
  Electron Density Fingerprints (EDprints): Virtual Screening Using Assembled Information of Electron Density. 1772-1780

Computational Chemistry

• 
  Guillem Revilla-López, Ana I. Jiménez, Carlos Cativiela, Ruth Nussinov, Carlos Alemán, David Zanuy:
  Conformational Profile of a Proline-Arginine Hybrid. 1781-1789
• 
  Anders Berglund, Richard D. Head:
  PZIM: A Method for Similarity Searching Using Atom Environments and 2D Alignment. 1790-1795
• 
  Seiji Hitaoka, Masataka Harada, Tatsusada Yoshida, Hiroshi Chuman:
  Correlation Analyses on Binding Affinity of Sialic Acid Analogues with Influenza Virus Neuraminidase-1 Using ab Initio MO Calculations on Their Complex Structures. 1796-1805
• 
  Carlos J. V. Simões, Trishna Mukherjee, Rui M. M. Brito, Richard M. Jackson:
  Toward the Discovery of Functional Transthyretin Amyloid Inhibitors: Application of Virtual Screening Methods. 1806-1820

Pharmaceutical Modeling

• 
  Johannes Mohr, Brijnesh J. Jain, Andreas Sutter, Antonius ter Laak, Thomas Steger-Hartmann, Nikolaus Heinrich, Klaus Obermayer:
  A Maximum Common Subgraph Kernel Method for Predicting the Chromosome Aberration Test. 1821-1838
• 
  Michal Brylinski, Jeffrey Skolnick:
  Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening. 1839-1854
• 
  Dengguo Wei, Hao Zheng, Naifang Su, Minghua Deng, Luhua Lai:
  Binding Energy Landscape Analysis Helps to Discriminate True Hits from High-Scoring Decoys in Virtual Screening. 1855-1864
• 
  Jacob D. Durrant, James Andrew McCammon:
  NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes. 1865-1871
• 
  George Papadatos, Muhammad Alkarouri, Valerie J. Gillet, Peter Willett, Visakan Kadirkamanathan, Christopher N. Luscombe, Gianpaolo Bravi, Nicola J. Richmond, Stephen D. Pickett, Jameed Hussain, John Pritchard, Anthony W. J. Cooper, Simon J. F. Macdonald:
  Lead Optimization Using Matched Molecular Pairs: Inclusion of Contextual Information for Enhanced Prediction of hERG Inhibition, Solubility, and Lipophilicity. 1872-1886
• 
  Dima A. Sabbah, Jonathan L. Vennerstrom, Haizhen Zhong:
  Docking Studies on Isoform-Specific Inhibition of Phosphoinositide-3-Kinases. 1887-1898

Bioinformatics

• 
  Nadine S. Schaadt, Jan Christoph, Volkhard Helms:
  Classifying Substrate Specificities of Membrane Transporters from Arabidopsis thaliana. 1899-1905
• 
  Nejc Carl, Janez Konc, Blaz Vehar, Dusanka Janezic:
  Protein-Protein Binding Site Prediction by Local Structural Alignment. 1906-1913

Volume 50, Number 11, November 2010

Perspective

• 
  Rabab Al Jishi, Peter Willett:
  The Journal of Chemical Documentation and the Journal of Chemical Information and Computer Sciences: Publication and Citation Statistics. 1915-1923

Chemical Information

• 
  Ruud van Deursen, Lorenz C. Blum, Jean-Louis Reymond:
  A Searchable Map of PubChem. 1924-1934
• 
  Anne Mai Wassermann, Britta Nisius, Martin Vogt, Jürgen Bajorath:
  Identification of Descriptors Capturing Compound Class-Specific Features by Mutual Information Analysis. 1935-1940

Computational Chemistry

• 
  Li Shao, Leihong Wu, Xiaohui Fan, Yiyu Cheng:
  Consensus Ranking Approach to Understanding the Underlying Mechanism With QSAR. 1941-1948
• 
  Haiying Yu, Ralph Kühne, Ralf-Uwe Ebert, Gerrit Schüürmann:
  Comparative Analysis of QSAR Models for Predicting pK_a of Organic Oxygen Acids and Nitrogen Bases from Molecular Structure. 1949-1960

Pharmaceutical Modeling

• 
  Christian Kramer, Peter Gedeck:
  Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets. 1961-1969
• 
  Qi Wang, Robert H. Mach, Robert R. Luedtke, David E. Reichert:
  Subtype Selectivity of Dopamine Receptor Ligands: Insights from Structure and Ligand-Based Methods. 1970-1985
• 
  Sudipto Mukherjee, Trent E. Balius, Robert C. Rizzo:
  Docking Validation Resources: Protein Family and Ligand Flexibility Experiments. 1986-2000
• 
  Gareth Jones:
  GAPE: An Improved Genetic Algorithm for Pharmacophore Elucidation. 2001-2018
• 
  Tam Luong Nguyen, Xiaoming Xu, Rick Gussio, Arun K. Ghosh, Ernest Hamel:
  The Assembly-Inducing Laulimalide/Peloruside A Binding Site on Tubulin: Molecular Modeling and Biochemical Studies with [³H]Peloruside A. 2019-2028
• 
  Robert P. Sheridan, Vladimir N. Maiorov, M. Katharine Holloway, Wendy D. Cornell, Ying-Duo Gao:
  Drug-like Density: A Method of Quantifying the "Bindability" of a Protein Target Based on a Very Large Set of Pockets and Drug-like Ligands from the Protein Data Bank. 2029-2040

Bioinformatics

• 
  Andrea Volkamer, Axel Griewel, Thomas Grombacher, Matthias Rarey:
  Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets. 2041-2052

Computer Software Reviews

• 
  George W. A. Milne:
  Software Review of ChemBioDraw 12.0. 2053

Volume 50, Number 12, December 2010

Chemical Information

• 
  Mohsen Kompany-Zareh, Nematollah Omidikia:
  Jackknife-Based Selection of Gram-Schmidt Orthogonalized Descriptors in QSAR. 2055-2066
• 
  Thibault Varin, Hanspeter Gubler, Christian N. Parker, Ji-Hu Zhang, Pichai Raman, Peter Ertl, Ansgar Schuffenhauer:
  Compound Set Enrichment: A Novel Approach to Analysis of Primary HTS Data. 2067-2078
• 
  Vishwesh Venkatraman, Violeta I. Pérez-Nueno, Lazaros Mavridis, David W. Ritchie:
  Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods. 2079-2093
• 
  Iurii Sushko, Sergii Novotarskyi, Robert Körner, Anil Kumar Pandey, Artem Cherkasov, Jiazhong Li, Paola Gramatica, Katja Hansen, Timon Schroeter, Klaus-Robert Müller, Lili Xi, Huanxiang Liu, Xiaojun Yao, Tomas Öberg, Farhad Hormozdiari, Phuong Dao, Süleyman Cenk Sahinalp, Roberto Todeschini, Pavel G. Polishchuk, Anatoly G. Artemenko, Victor Kuzmin, Todd Martin, Douglas M. Young, Denis Fourches, Eugene N. Muratov, Alexander Tropsha, Igor I. Baskin, Dragos Horvath, Gilles Marcou, Christophe Muller, Alexandre Varnek, Volodymyr V. Prokopenko, Igor V. Tetko:
  Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. 2094-2111
• 
  Ye Hu, Jürgen Bajorath:
  Polypharmacology Directed Compound Data Mining: Identification of Promiscuous Chemotypes with Different Activity Profiles and Comparison to Approved Drugs. 2112-2118

Computational Chemistry

• 
  Sharangdhar S. Phatak, Edgar A. Gatica, Claudio N. Cavasotto:
  Ligand-Steered Modeling and Docking: A Benchmarking Study in Class A G-Protein-Coupled Receptors. 2119-2128
• 
  Jorge M. C. Marques, J. L. Llanio-Trujillo, P. E. Abreu, Francisco Baptista Pereira:
  How Different Are Two Chemical Structures? 2129-2140
• 
  Hongming Chen, Yidong Yang, Ola Engkvist:
  Molecular Topology Analysis of the Differences between Drugs, Clinical Candidate Compounds, and Bioactive Molecules. 2141-2150
• 
  Halina Szatylowicz, Nina Sadlej-Sosnowska:
  Characterizing the Strength of Individual Hydrogen Bonds in DNA Base Pairs. 2151-2161
• 
  Gabriella Ortore, Tiziano Tuccinardi, Elisabetta Orlandini, Adriano Martinelli:
  Different Binding Modes of Structurally Diverse Ligands for Human D3DAR. 2162-2175
• 
  Verónica A. Jiménez:
  Quantum-Chemical Study on the Bioactive Conformation of Epothilones. 2176-2190

Computational Biochemistry

• 
  Peter Schmidtke, Catherine Souaille, Frédéric Estienne, Nicolas Baurin, Romano T. Kroemer:
  Large-Scale Comparison of Four Binding Site Detection Algorithms. 2191-2200
• 
  Zhili Zuo, Neha Gandhi, Ricardo L. Mancera:
  Calculations of the Free Energy of Interaction of the c-Fos-c-Jun Coiled Coil: Effects of the Solvation Model and the Inclusion of Polarization Effects. 2201-2212
• 
  David N. Langelaan, Michal Wieczorek, Christian Blouin, Jan K. Rainey:
  Improved Helix and Kink Characterization in Membrane Proteins Allows Evaluation of Kink Sequence Predictors. 2213-2220
• 
  Justin A. Lemkul, William J. Allen, David R. Bevan:
  Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies. 2221-2235
• 
  Binh Khanh Mai, Man Hoang Viet, Mai Suan Li:
  Top Leads for Swine Influenza A/H1N1 Virus Revealed by Steered Molecular Dynamics Approach. 2236-2247

Pharmaceutical Modeling

• 
  Edward J. Bertaccini, Björn Wallner, James R. Trudell, Erik Lindahl:
  Modeling Anesthetic Binding Sites within the Glycine Alpha One Receptor Based on Prokaryotic Ion Channel Templates: The Problem with TM4. 2248-2255
• 
  Tamar Traube, Vijayakumar Subramaniam, Michal Hirsch, Neta Uritsky, Michael Shokhen, Amnon Albeck:
  EMBM - A New Enzyme Mechanism-Based Method for Rational Design of Chemical Sites of Covalent Inhibitors. 2256-2265

Bioinformatics

• 
  Shrihari Sonavane, Pinak Chakrabarti:
  Prediction of Active Site Cleft Using Support Vector Machines. 2266-2273

Errata

• 
  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. 2274