Journal of Chemical Information and Modeling, Volume 45

Volume 45, Number 1, January 2005

Editorial

• 
  William L. Jorgensen:
  Journal of Chemical Information and Modeling. 1

Articles - Chemical Information

• 
  Atipat Rojnuckarin, Daniel A. Gschwend, Sergio H. Rotstein, David S. Hartsough:
  ArQiologist: An Integrated Decision Support Tool for Lead Optimization. 2-9

Computational Chemistry

• 
  Zhenming Liu, Changkang Huang, Keqiang Fan, Ping Wei, Hao Chen, Shiyong Liu, Jianfeng Pei, Lei Shi, Bo Li, Kun Yang, Ying Liu, Luhua Lai:
  Virtual Screening of Novel Noncovalent Inhibitors for SARS-CoV 3C-like Proteinase. 10-17
• 
  Tomasz Spalek, Piotr Pietrzyk, Zbigniew Sojka:
  Application of the Genetic Algorithm Joint with the Powell Method to Nonlinear Least-Squares Fitting of Powder EPR Spectra. 18-29
• 
  Matthew Clark:
  Generalized Fragment-Substructure Based Property Prediction Method. 30-38
• 
  Jaroslaw J. Panek, Aneta Jezierska, Krzysztof Mierzwicki, Zdzislaw Latajka, Aleksander Koll:
  Molecular Modeling Study of Leflunomide and Its Active Metabolite Analogues. 39-48
• 
  Karthigeyan Nagarajan, Randy J. Zauhar, William J. Welsh:
  Enrichment of Ligands for the Serotonin Receptor Using the Shape Signatures Approach. 49-57
• 
  Sasa Kovacic, Antonija Lesar, Milan Hodoscek:
  Quantum Mechanical Study of the Potential Energy Surface of the ClO + NO₂ Reaction. 58-64
• 
  Rajarshi Guha, Peter C. Jurs:
  Determining the Validity of a QSAR Model - A Classification Approach. 65-73
• 
  Christoph Rücker, Markus Meringer, Adalbert Kerber:
  QSPR Using MOLGEN-QSPR: The Challenge of Fluoroalkane Boiling Points. 74-80
• 
  K. M. Nalin de Silva, Jonathan M. Goodman:
  What Is the Smallest Saturated Acyclic Alkane that Cannot Be Made?. 81-87
• 
  Wei Zhang, Tingjun Hou, Xiaojie Xu:
  New Born Radii Deriving Method for Generalized Born Model. 88-93
• 
  Iiris Kahn, Dan C. Fara, Mati Karelson, Uko Maran, Patrik L. Andersson:
  QSPR Treatment of the Soil Sorption Coefficients of Organic Pollutants. 94-105

Computational Biochemistry

• 
  Tatiana I. Netzeva, Aynur O. Aptula, Emilio Benfenati, Mark T. D. Cronin, Giuseppina C. Gini, Iglika Lessigiarska, Uko Maran, Marjan Vracko, Gerrit Schüürmann:
  Description of the Electronic Structure of Organic Chemicals Using Semiempirical and Ab Initio Methods for Development of Toxicological QSARs. 106-114
• 
  Chun Li, Jun Wang:
  New Invariant of DNA Sequences. 115-120
• 
  Huabei Zhang:
  A New Approach for the Tissue-Blood Partition Coefficients of Neutral and Ionized Compounds. 121-127
• 
  Edward J. Bertaccini, Jessica Shapiro, Douglas L. Brutlag, James R. Trudell:
  Homology Modeling of a Human Glycine Alpha 1 Receptor Reveals a Plausible Anesthetic Binding Site. 128-135
• 
  Philip Prathipati, Gyanendra Pandey, Anil K. Saxena:
  CoMFA and Docking Studies on Glycogen Phosphorylase a Inhibitors as Antidiabetic Agents. 136-145
• 
  Eva M. Krovat, Karin H. Frühwirth, Thierry Langer:
  Pharmacophore Identification, in Silico Screening, and Virtual Library Design for Inhibitors of the Human Factor Xa. 146-159

Pharmaceutical Modeling

• 
  Gerhard Wolber, Thierry Langer:
  LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters. 160-169
• 
  Cornel Catana, Hua Gao, Christian Orrenius, Pieter F. W. Stouten:
  Linear and Nonlinear Methods in Modeling the Aqueous Solubility of Organic Compounds. 170-176
• 
  John J. Irwin, Brian K. Shoichet:
  ZINC - A Free Database of Commercially Available Compounds for Virtual Screening. 177-182

Bioinformatics

• 
  Mauro Colafranceschi, Alfredo Colosimo, Joseph P. Zbilut, Vladimir N. Uversky, Alessandro Giuliani:
  Structure-Related Statistical Singularities along Protein Sequences: A Correlation Study. 183-189
• 
  Bahram Hemmateenejad, Mohammad A. Safarpour, Ramin Miri, Nasim Nesari:
  Toward an Optimal Procedure for PC-ANN Model Building: Prediction of the Carcinogenic Activity of a Large Set of Drugs. 190-199
• 
  Simon Spycher, Eric Pellegrini, Johann Gasteiger:
  Use of Structure Descriptors To Discriminate between Modes of Toxic Action of Phenols. 200-208

Software Review

• 
  Beth Thomsett-Scott:
  Origin 7.5. 209-210
• 
  Stephen R. Heller:
  ACT! 2005. 211
• 
  David J. Wild:
  MINITAB Release 14. 212

Volume 45, Number 2, March 2005

Articles - Chemical Information

• 
  Paul Labute:
  On the Perception of Molecules from 3D Atomic Coordinates. 215-221
• 
  Ivan Gutman, Pierre Hansen, Hadrien Mélot:
  Variable Neighborhood Search for Extremal Graphs. 10. Comparison of Irregularity Indices for Chemical Trees. 222-230
• 
  Gonzalo Cerruela García, Irene Luque Ruiz, Miguel Ángel Gómez-Nieto, Juan Antonio Cabrero Doncel, Antonio Guevara Plaza:
  From Wiener Index to Molecules. 231-238
• 
  Stephan C. Schürer, Prashant Tyagi, Steven M. Muskal:
  Prospective Exploration of Synthetically Feasible, Medicinally Relevant Chemical Space. 239-248
• 
  Klaus-Robert Müller, Gunnar Rätsch, Sören Sonnenburg, Sebastian Mika, Michael Grimm, Nikolaus Heinrich:
  Classifying 'Drug-likeness' with Kernel-Based Learning Methods. 249-253

Computational Chemistry

• 
  Youngyong In, Han Ha Chai, Kyoung Tai No:
  A Partition Coefficient Calculation Method with the SFED Model. 254-263
• 
  Jaroslaw J. Panek, Aneta Jezierska, Marjan Vracko:
  Kohonen Network Study of Aromatic Compounds Based on Electronic and Nonelectronic Structure Descriptors. 264-272
• 
  Michael E. Beck:
  Do Fukui Function Maxima Relate to Sites of Metabolism? A Critical Case Study. 273-282
• 
  Ovanes Mekenyan, Todor Pavlov, Vanjo Grancharov, Milen Todorov, Patricia Schmieder, Gilman Veith:
  2D-3D Migration of Large Chemical Inventories with Conformational Multiplication. Application of the Genetic Algorithm. 283-292
• 
  Mircea V. Diudea, Csaba L. Nagy, Ioan Silaghi-Dumitrescu, Ante Graovac, Dusanka Janezic, Drazen Vikic-Topic:
  Periodic Cages. 293-299
• 
  Kitiyaporn Wittayanarakul, Ornjira Aruksakunwong, Pornthep Sompornpisut, Vannajan Sanghiran Lee, Vudhichai Parasuk, Surapong Pinitglang, Supot Hannongbua:
  Structure, Dynamics and Solvation of HIV-1 Protease/Saquinavir Complex in Aqueous Solution and Their Contributions to Drug Resistance: Molecular Dynamic Simulations. 300-308
• 
  Jure Zupan, Milan Randic:
  Algorithm for Coding DNA Sequences into "Spectrum-like" and "Zigzag" Representations. 309-313
• 
  Nikolay P. Todorov, Christoph L. Buenemann, Ian L. Alberts:
  Combinatorial Ligand Design Targeted at Protein Families. 314-320
• 
  Ana Gallegos, Xavier Gironés:
  Topological Quantum Similarity Indices Based on Fitted Densities: Theoretical Background and QSPR Application. 321-326
• 
  Ivo Cacelli, Silvio Campanile, Alessandro Giolitti, Dafne Molin:
  Theoretical Prediction of the Abraham Hydrogen Bond Acidity and Basicity Factors from a Reaction Field Method. 327-333
• 
  Igor Novak:
  Molecular Modeling of Anti-Bredt Compounds. 334-338
• 
  Orsolya Farkas, Károly Héberger:
  Comparison of Ridge Regression, Partial Least-Squares, Pairwise Correlation, Forward- and Best Subset Selection Methods for Prediction of Retention Indices for Aliphatic Alcohols. 339-346
• 
  Qishi Du, Peng-Jun Liu, Paul G. Mezey:
  Theoretical Derivation of Heuristic Molecular Lipophilicity Potential: A Quantum Chemical Description for Molecular Solvation. 347-353
• 
  Norberto Castillo, Chérif F. Matta, Russell J. Boyd:
  Fluorine-Fluorine Spin-Spin Coupling Constants in Aromatic Compounds: Correlations with the Delocalization Index and with the Internuclear Separation. 354-359
• 
  Laura K. Schnackenberg, Richard D. Beger:
  Whole-Molecule Calculation of Log P Based on Molar Volume, Hydrogen Bonds, and Simulated ¹³C NMR Spectra. 360-365
• 
  Marjan A. Rafiee, Nasser L. Hadipour, Hossein Naderi-manesh:
  The Role of Charge Distribution on the Antimalarial Activity of Artemisinin Analogues. 366-370
• 
  Fei Cai, Heqing Shao, Chungen Liu, Yuansheng Jiang:
  An Alternative Strategy for Count and Storage of Kekulé and Longer Range Resonance Valence Bond Structures. 371-378

Computational Biochemistry

• 
  Martin Smiesko, Emilio Benfenati:
  Thermodynamic Descriptors Derived from Density Functional Theory Calculations in Prediction of Aquatic Toxicity. 379-385
• 
  David Vidal, Michael Thormann, Miquel Pons:
  LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities. 386-393
• 
  Janez Strancar, Tilen Koklic, Zoran Arsov, Bogdan Filipic, David Stopar, Marcus A. Hemminga:
  Spin Label EPR-Based Characterization of Biosystem Complexity. 394-406
• 
  Kuo-Chen Chou, Yu-Dong Cai:
  Prediction of Membrane Protein Types by Incorporating Amphipathic Effects. 407-413
• 
  Christian Hofbauer, András Aszódi:
  SH2 Binding Site Comparison: A New Application of the SURFCOMP Method. 414-421

Pharmaceutical Modeling

• 
  Johannes Kirchmair, Christian Laggner, Gerhard Wolber, Thierry Langer:
  Comparative Analysis of Protein-Bound Ligand Conformations with Respect to Catalyst's Conformational Space Subsampling Algorithms. 422-430
• 
  Daniela Schuster, Thierry Langer:
  The Identification of Ligand Features Essential for PXR Activation by Pharmacophore Modeling. 431-439
• 
  Huabei Zhang, Hua Li, Chunping Liu:
  CoMFA, CoMSIA, and Molecular Hologram QSAR Studies of Novel Neuronal nAChRs Ligands-Open Ring Analogues of 3-Pyridyl Ether. 440-448
• 
  Markus H. J. Seifert:
  ProPose: Steered Virtual Screening by Simultaneous Protein-Ligand Docking and Ligand-Ligand Alignment. 449-460
• 
  Rajendra Kristam, Valerie J. Gillet, Richard A. Lewis, David A. Thorner:
  Comparison of Conformational Analysis Techniques To Generate Pharmacophore Hypotheses Using Catalyst. 461-476
• 
  Bernard Pirard, Joachim Brendel, Stefan Peukert:
  The Discovery of Kv1.5 Blockers as a Case Study for the Application of Virtual Screening Approaches. 477-485

Bioinformatics

• 
  Wei-Qi Lin, Jian-Hui Jiang, Qi Shen, Guo-Li Shen, Ru-Qin Yu:
  Optimized Block-wise Variable Combination by Particle Swarm Optimization for Partial Least Squares Modeling in Quantitative Structure-Activity Relationship Studies. 486-493
• 
  M. Michael Gromiha:
  A Statistical Model for Predicting Protein Folding Rates from Amino Acid Sequence with Structural Class Information. 494-501
• 
  Santiago Vilar, Ernesto Estrada, Eugenio Uriarte, Lourdes Santana, Yaquelin Gutierrez:
  In Silico Studies toward the Discovery of New Anti-HIV Nucleoside Compounds through the Use of TOPS-MODE and 2D/3D Connectivity Indices. 2. Purine Derivatives. 502-514

Software Description

• 
  Kejun Liu, Jun Feng, S. Stanley Young:
  PowerMV: A Software Environment for Molecular Viewing, Descriptor Generation, Data Analysis and Hit Evaluation. 515-522
• 
  Christopher Kibbey, Alain Calvet:
  Molecular Property eXplorer: A Novel Approach to Visualizing SAR Using Tree-Maps and Heatmaps. 523-532

Errata

• 
  Alan R. Katritzky, Ritu Jain, Andre Lomaka, Ruslan Petrukhin, Mati Karelson, Ann E. Visser, Robin D. Rogers:
  Correlation of the Melting Points of Potential Ionic Liquids (Imidazolium Bromides and Benzimidazolium Bromides) Using the CODESSA Program [J. Chem. Inf. Comput. Sci. 42, 225-231 (2002)]. 533-534
• 
  Tomas Öberg:
  Boiling Points of Halogenated Aliphatic Compounds: A Quantitative Structure-Property Relationship for Prediction and Validation [J. Chem. Inf. Comput. Sci. 44, 187-192 (2004)]. 534

Volume 45, Number 3, May 2005

Articles Chemical Information

• 
  Wei-Qi Lin, Jian-Hui Jiang, Qi Shen, Hai-Long Wu, Guo-Li Shen, Ru-Qin Yu:
  Piecewise Hypersphere Modeling by Particle Swarm Optimization in QSAR Studies of Bioactivities of Chemical Compounds. 535-541
• 
  Martin Stahl, Harald Mauser:
  Database Clustering with a Combination of Fingerprint and Maximum Common Substructure Methods. 542-548
• 
  Robert N. Jorissen, Michael K. Gilson:
  Virtual Screening of Molecular Databases Using a Support Vector Machine. 549-561
• 
  Jerry Ray Dias:
  Perimeter Topology of Benzenoid Polycyclic Hydrocarbons. 562-571
• 
  Muthukumarasamy Karthikeyan, Andreas Bender:
  Encoding and Decoding Graphical Chemical Structures as Two-Dimensional (PDF417) Barcodes. 572-580

Computational Chemistry

• 
  Muthukumarasamy Karthikeyan, Robert C. Glen, Andreas Bender:
  General Melting Point Prediction Based on a Diverse Compound Data Set and Artificial Neural Networks. 581-590
• 
  Tulay Ercanli, Donald B. Boyd:
  Evaluation of Computational Chemistry Methods: Crystallographic and Cheminformatics Analysis of Aminothiazole Methoximes. 591-601
• 
  Stefano Alcaro, Francesco Ortuso, Robert S. Coleman:
  Molecular Modeling of DNA Cross-linking Analogues Based on the Azinomycin Scaffold. 602-609
• 
  Milind Misra, Amit Banerjee, Rajesh N. Davé, Carol A. Venanzi:
  Novel Feature Extraction Technique for Fuzzy Relational Clustering of a Flexible Dopamine Reuptake Inhibitor. 610-623
• 
  Alfonso T. García-Sosa, Stuart Firth-Clark, Ricardo L. Mancera:
  Including Tightly-Bound Water Molecules in de Novo Drug Design. Exemplification through the in Silico Generation of Poly(ADP-ribose)polymerase Ligands. 624-633
• 
  Filip Fratev, Emilio Benfenati:
  3D-QSAR and Molecular Mechanics Study for the Differences in the Azole Activity against Yeastlike and Filamentous Fungi and Their Relation to P450DM Inhibition. 1. 3-Substituted-4(3H)-quinazolinones. 634-644
• 
  Alessandra Rodrigues Rufino, Antônio J. C. Brant, João B. O. Santos, Marcelo J. P. Ferreira, Vicente de Paulo Emerenciano:
  Simple Method for Identification of Skeletons of Aporphine Alkaloids from ¹³C NMR Data Using Artificial Neural Networks. 645-651
• 
  Tadeusz Marek Krygowski, Halina Szatylowicz, Joanna E. Zachara:
  Molecular Geometry as a Source of Chemical Information. 5. Substituent Effect on Proton Transfer in Para-Substituted Phenol Complexes with Fluoride-a B3LYP/6-311+G** Study. 652-656
• 
  Yegor Zyrianov:
  Distribution-Based Descriptors of the Molecular Shape. 657-672
• 
  James A. Haigh, Barry T. Pickup, J. Andrew Grant, Anthony Nicholls:
  Small Molecule Shape-Fingerprints. 673-684
• 
  Philippe Vismara, Yannic S. Tognetti, Claude Laurenço:
  Maximum Symmetrical Split of Molecular Graphs. Application to Organic Synthesis Design. 685-695

Computational Biochemistry

• 
  Martin J. Bayley, Eleanor J. Gardiner, Peter Willett, Peter J. Artymiuk:
  A Fourier Fingerprint-Based Method for Protein Surface Representation. 696-707

Pharmaceutical Modeling

• 
  Elodie Lescot, Ronan Bureau, Jana Sopkova-de Oliveira Santos, Christophe Rochais, Vincent Lisowski, Jean-Charles Lancelot, Sylvain Rault:
  3D-QSAR and Docking Studies of Selective GSK-3beta Inhibitors. Comparison with a Thieno[2, 3-b]pyrrolizinone Derivative, a New Potential Lead for GSK-3beta Ligands. 708-715
• 
  Theodora M. Steindl, Christian Laggner, Thierry Langer:
  Human Rhinovirus 3C Protease: Generation of Pharmacophore Models for Peptidic and Nonpeptidic Inhibitors and Their Application in Virtual Screening. 716-724
• 
  Vema Aparna, G. Rambabu, Sunil K. Panigrahi, J. A. R. P. Sarma, Gautam R. Desiraju:
  Virtual Screening of 4-Anilinoquinazoline Analogues as EGFR Kinase Inhibitors: Importance of Hydrogen Bonds in the Evaluation of Poses and Scoring Functions. 725-738
• 
  Nikolaus Stiefl, Knut Baumann:
  Structure-Based Validation of the 3D-QSAR Technique MaP. 739-749
• 
  Yong-Hua Wang, Yan Li, Sheng-Li Yang, Ling Yang:
  Classification of Substrates and Inhibitors of P-Glycoprotein Using Unsupervised Machine Learning Approach. 750-757
• 
  Céline Le Bailly de Tilleghem, Benoît Beck, Bruno Boulanger, Bernadette Govaerts:
  A Fast Exchange Algorithm for Designing Focused Libraries in Lead Optimization. 758-767
• 
  T. John McNeany, Jonathan D. Hirst:
  Inhibition of the Tyrosine Kinase, Syk, Analyzed by Stepwise Nonparametric Regression. 768-776
• 
  Peter Itskowitz, Alexander Tropsha:
  k Nearest Neighbors QSAR Modeling as a Variational Problem: Theory and Applications. 777-785
• 
  Vladimir Svetnik, Ting Wang, Christopher Tong, Andy Liaw, Robert P. Sheridan, Qinghua Song:
  Boosting: An Ensemble Learning Tool for Compound Classification and QSAR Modeling. 786-799

Bioinformatics

• 
  Rajarshi Guha, Peter C. Jurs:
  Interpreting Computational Neural Network QSAR Models: A Measure of Descriptor Importance. 800-806

Volume 45, Number 4, July 2005

Articles Chemical Information

• 
  Alexander Böcker, Swetlana Derksen, Elena Schmidt, Andreas Teckentrup, Gisbert Schneider:
  A Hierarchical Clustering Approach for Large Compound Libraries. 807-815
• 
  Michael Frenkel, Robert D. Chirico, Vladimir V. Diky, Xinjian Yan, Qian Dong, Chris Muzny:
  ThermoData Engine (TDE): Software Implementation of the Dynamic Data Evaluation Concept. 816-838
• 
  Sabcho Dimitrov, Gergana Dimitrova, Todor Pavlov, Nadezhda Dimitrova, Grace Patlewicz, Jay Niemela, Ovanes Mekenyan:
  A Stepwise Approach for Defining the Applicability Domain of SAR and QSAR Models. 839-849
• 
  Lijie Wang, Peter Warburton, Zsolt Szekeres, Peter Surjan, Paul G. Mezey:
  Stability and Properties of Polyhelicenes and Annelated Fused-Ring Carbon Helices: Models Toward Helical Graphites. 850-855
• 
  Suxin Zheng, Xiaomin Luo, Gang Chen, Weiliang Zhu, Jianhua Shen, Kaixian Chen, Hualiang Jiang:
  A New Rapid and Effective Chemistry Space Filter in Recognizing a Druglike Database. 856-862
• 
  Robin Hewitt, Alberto Gobbi, Man-Ling Lee:
  A Searching and Reporting System for Relational Databases Using a Graph-Based Metadata Representation. 863-869
• 
  Teodora Ivanciuc, Ovidiu Ivanciuc, Douglas J. Klein:
  Posetic Quantitative Superstructure/Activity Relationships (QSSARs) for Chlorobenzenes. 870-879

Computational Chemistry

• 
  Peter Zinn:
  Adaptive Multicomponent Analysis by Genetic Algorithms. 880-887
• 
  Sorel Muresan, Jens Sadowski:
  "In-House Likeness": Comparison of Large Compound Collections Using Artificial Neural Networks. 888-893
• 
  César Hervás-Martínez, Alfonso Carlos Martínez-Estudillo, Manuel Silva, Juan Manuel Serrano:
  Improving the Quantification of Highly Overlapping Chromatographic Peaks by Using Product Unit Neural Networks Modeled by an Evolutionary Algorithm. 894-903
• 
  Frances V. Buontempo, Xue Zhong Wang, Mulaisho Mwense, Nigel Horan, Anita Young, Daniel Osborn:
  Genetic Programming for the Induction of Decision Trees to Model Ecotoxicity Data. 904-912
• 
  Alan R. Katritzky, Indrek Tulp, Dan C. Fara, Antonino Lauria, Uko Maran, William E. Acree Jr.:
  A General Treatment of Solubility. 3. Principal Component Analysis (PCA) of the Solubilities of Diverse Solutes in Diverse Solvents. 913-923
• 
  Matthew D. Miller, David M. Yourtee, Alan G. Glaros, Cecil C. Chappelow, J. David Eick, Andrew J. Holder:
  Quantum Mechanical Structure-Activity Relationship Analyses for Skin Sensitization. 924-929
• 
  Milan Soskic, Dejan Plavsic:
  Modeling the Octanol-Water Partition Coefficients by an Optimized Molecular Connectivity Index. 930-938
• 
  Pierre Mahé, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, Jean-Philippe Vert:
  Graph Kernels for Molecular Structure-Activity Relationship Analysis with Support Vector Machines. 939-951
• 
  Shengqiao Li, Adam Fedorowicz, Harshinder Singh, Sidney C. Soderholm:
  Application of the Random Forest Method in Studies of Local Lymph Node Assay Based Skin Sensitization Data. 952-964
• 
  Corneliu Buda, Abul B. Kazi, Adriana Dinescu, Thomas R. Cundari:
  Stability Studies of Transition-Metal Linkage Isomers Using Quantum Mechanical Methods. Groups 11 and 12 Transition Metals. 965-970
• 
  James L. Melville, Kevin R. J. Lovelock, Claire Wilson, Bryan Allbutt, Edmund K. Burke, Barry Lygo, Jonathan D. Hirst:
  Exploring Phase-Transfer Catalysis with Molecular Dynamics and 3D/4D Quantitative Structure-Selectivity Relationships. 971-981
• 
  Chun Wei Yap, Yu Zong Chen:
  Prediction of Cytochrome P450 3A4, 2D6, and 2C9 Inhibitors and Substrates by Using Support Vector Machines. 982-992
•