Volume 45, Number 1, January 2005

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

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

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  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
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  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
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  Matthew Clark: Generalized Fragment-Substructure Based Property Prediction Method. 30-38
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  Jaroslaw J. Panek, Aneta Jezierska, Krzysztof Mierzwicki, Zdzislaw Latajka, Aleksander Koll: Molecular Modeling Study of Leflunomide and Its Active Metabolite Analogues. 39-48
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  Karthigeyan Nagarajan, Randy J. Zauhar, William J. Welsh: Enrichment of Ligands for the Serotonin Receptor Using the Shape Signatures Approach. 49-57
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  Sasa Kovacic, Antonija Lesar, Milan Hodoscek: Quantum Mechanical Study of the Potential Energy Surface of the ClO + NO₂ Reaction. 58-64
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  Rajarshi Guha, Peter C. Jurs: Determining the Validity of a QSAR Model - A Classification Approach. 65-73
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  Christoph Rücker, Markus Meringer, Adalbert Kerber: QSPR Using MOLGEN-QSPR: The Challenge of Fluoroalkane Boiling Points. 74-80
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  K. M. Nalin de Silva, Jonathan M. Goodman: What Is the Smallest Saturated Acyclic Alkane that Cannot Be Made?. 81-87
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  Wei Zhang, Tingjun Hou, Xiaojie Xu: New Born Radii Deriving Method for Generalized Born Model. 88-93
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  Iiris Kahn, Dan C. Fara, Mati Karelson, Uko Maran, Patrik L. Andersson: QSPR Treatment of the Soil Sorption Coefficients of Organic Pollutants. 94-105

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  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
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  Chun Li, Jun Wang: New Invariant of DNA Sequences. 115-120
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  Huabei Zhang: A New Approach for the Tissue-Blood Partition Coefficients of Neutral and Ionized Compounds. 121-127
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  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
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  Philip Prathipati, Gyanendra Pandey, Anil K. Saxena: CoMFA and Docking Studies on Glycogen Phosphorylase a Inhibitors as Antidiabetic Agents. 136-145
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  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

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

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  Mauro Colafranceschi, Alfredo Colosimo, Joseph P. Zbilut, Vladimir N. Uversky, Alessandro Giuliani: Structure-Related Statistical Singularities along Protein Sequences: A Correlation Study. 183-189
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  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
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  Simon Spycher, Eric Pellegrini, Johann Gasteiger: Use of Structure Descriptors To Discriminate between Modes of Toxic Action of Phenols. 200-208

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

Volume 45, Number 2, March 2005

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

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  Youngyong In, Han Ha Chai, Kyoung Tai No: A Partition Coefficient Calculation Method with the SFED Model. 254-263
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  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
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  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
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  Mircea V. Diudea, Csaba L. Nagy, Ioan Silaghi-Dumitrescu, Ante Graovac, Dusanka Janezic, Drazen Vikic-Topic: Periodic Cages. 293-299
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  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
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  Jure Zupan, Milan Randic: Algorithm for Coding DNA Sequences into "Spectrum-like" and "Zigzag" Representations. 309-313
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  Nikolay P. Todorov, Christoph L. Buenemann, Ian L. Alberts: Combinatorial Ligand Design Targeted at Protein Families. 314-320
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  Anna Gallegos, Xavier Gironés: Topological Quantum Similarity Indices Based on Fitted Densities: Theoretical Background and QSPR Application. 321-326
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  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
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  Igor Novak: Molecular Modeling of Anti-Bredt Compounds. 334-338
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  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
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  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
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  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
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  Marjan A. Rafiee, Nasser L. Hadipour, Hossein Naderi-manesh: The Role of Charge Distribution on the Antimalarial Activity of Artemisinin Analogues. 366-370
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  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

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

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  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
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  Daniela Schuster, Thierry Langer: The Identification of Ligand Features Essential for PXR Activation by Pharmacophore Modeling. 431-439
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  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
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  Rajendra Kristam, Valerie J. Gillet, Richard A. Lewis, David A. Thorner: Comparison of Conformational Analysis Techniques To Generate Pharmacophore Hypotheses Using Catalyst. 461-476
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  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

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  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
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  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

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

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  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
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  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

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  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
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  Muthukumarasamy Karthikeyan, Andreas Bender: Encoding and Decoding Graphical Chemical Structures as Two-Dimensional (PDF417) Barcodes. 572-580

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  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
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  Stefano Alcaro, Francesco Ortuso, Robert S. Coleman: Molecular Modeling of DNA Cross-linking Analogues Based on the Azinomycin Scaffold. 602-609
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  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
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  Alessandra R. 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
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  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

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

• 
  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

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

Volume 45, Number 4, July 2005

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  Alexander Böcker, Swetlana Derksen, Elena Schmidt, Andreas Teckentrup, Gisbert Schneider: A Hierarchical Clustering Approach for Large Compound Libraries. 807-815
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  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
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  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

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  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, 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
• 
  Simon S. J. Cross: Improved FlexX Docking Using FlexS-Determined Base Fragment Placement. 993-1001
• 
  Mircea V. Diudea: Nanoporous Carbon Allotropes by Septupling Map Operations. 1002-1009
• 
  Jr-Hung Lin, Timothy Clark: Nanoporous Carbon Allotropes by Septupling Map Operations. 1010-1016
• 
  Vladimir N. Maiorov, Robert P. Sheridan: Enhanced Virtual Screening by Combined Use of Two Docking Methods: Getting the Most on a Limited Budget. 1017-1023

• 
  Qi Shen, Jian-Hui Jiang, Jing-chao Tao, Guo-Li Shen, Ru-Qin Yu: Modified Ant Colony Optimization Algorithm for Variable Selection in QSAR Modeling: QSAR Studies of Cyclooxygenase Inhibitors. 1024-1029
• 
  Jan Cz. Dobrowolski, Aleksander P. Mazurek: Model Carbyne vs Ideal and DNA Catenanes. 1030-1038

• 
  Harald Mauser, Olivier Roche, Martin Stahl, Stephan Müller: Prediction of UV and ESI-MS Signal Intensities. 1039-1046
• 
  Brian S. Henriksen, Todd J. Zahn, Jeffrey D. Evanseck, Steven M. Firestine, Richard A. Gibbs: Computational and Conformational Evaluation of FTase Alternative Substrates: Insight into a Novel Enzyme Binding Pocket. 1047-1052
• 
  Bernd Ehresmann, Marcel J. de Groot, Timothy Clark: Surface-Integral QSPR Models: Local Energy Properties. 1053-1060
• 
  Chidochangu P. Mpamhanga, Beining Chen, Iain M. McLay, Daniel L. Ormsby, Mika K. Lindvall: Retrospective Docking Study of PDE4B Ligands and an Analysis of the Behavior of Selected Scoring Functions. 1061-1074
• 
  Alban Lepailleur, Ronan Bureau, Magalie Paillet-Loilier, Frédéric Fabis, Nicolas Saettel, Stéphane Lemaître, François Dauphin, Aurélien Lesnard, Jean-Charles Lancelot, Sylvain Rault: Molecular Modeling Studies Focused on 5-HT₇ versus 5-HT_1A Selectivity. Discovery of Novel Phenylpyrrole Derivatives with High Affinity for 5-HT₇ Receptors. 1075-1081
• 
  Yovani Marrero-Ponce, Maité Iyarreta-Veitía, Alina Montero-Torres, Carlos Romero-Zaldivar, Carlos A. Brandt, Priscilla E. Ávila, Karin Kirchgatter, Yanetsy Machado: Ligand-Based Virtual Screening and in Silico Design of New Antimalarial Compounds Using Nonstochastic and Stochastic Total and Atom-Type Quadratic Maps. 1082-1100
• 
  B. Gopalakrishnan, V. Aparna, J. Jeevan, M. Ravi, G. R. Desiraju: A Virtual Screening Approach for Thymidine Monophosphate Kinase Inhibitors as Antitubercular Agents Based on Docking and Pharmacophore Models. 1101-1108
• 
  Rajarshi Guha, David T. Stanton, Peter C. Jurs: Interpreting Computational Neural Network Quantitative Structure-Activity Relationship Models: A Detailed Interpretation of the Weights and Biases. 1109-1121
• 
  Jamal C. Saeh, Paul D. Lyne, Bryan K. Takasaki, David A. Cosgrove: Lead Hopping Using SVM and 3D Pharmacophore Fingerprints. 1122-1133

• 
  Jinn-Moon Yang, Yen-Fu Chen, Tsai-Wei Shen, Bruce S. Kristal, D. Frank Hsu: Consensus Scoring Criteria for Improving Enrichment in Virtual Screening. 1134-1146
• 
  Pasak Senawongse, Andrew R. Dalby, Zheng Rong Yang: Predicting the Phosphorylation Sites Using Hidden Markov Models and Machine Learning Methods. 1147-1152

Volume 45, Number 5, September 2005

• 
  Boris L. Milman: Literature-Based Generation of Hypotheses on Chemical Composition Using Database Co-occurrence of Chemical Compounds. 1153-1158
• 
  Christian Merkwirth, Thomas Lengauer: Automatic Generation of Complementary Descriptors with Molecular Graph Networks. 1159-1168
• 
  Martin Hornig, Andreas Klamt: COSMOfrag: A Novel Tool for High-Throughput ADME Property Prediction and Similarity Screening Based on Quantum Chemistry. 1169-1177
• 
  Irene Luque Ruiz, Gonzalo Cerruela García, Miguel Ángel Gómez-Nieto: Clustering Chemical Databases Using Adaptable Projection Cells and MCS Similarity Values. 1178-1194
• 
  John W. Raymond, Christopher E. Kibbey: An Automated Method for Exploring Targeted Substructural Diversity within Sets of Chemical Structures. 1195-1204
• 
  Milan Randic, Marjana Novic, Marjan Vracko: Novel Characterization of Proteomics Maps by Sequential Neighborhoods of Protein Spots. 1205-1213
• 
  Qian Zhu, Jianhua Yao, Shengang Yuan, Feng Li, Haifeng Chen, Wei Cai, Quan Liao: Superstructure Searching Algorithm for Generic Reaction Retrieval. 1214-1222
• 
  Daniel J. Graham: Information Content in Organic Molecules: Aggregation States and Solvent Effects. 1223-1236
• 
  Tharun Kumar Allu, Tudor I. Oprea: Rapid Evaluation of Synthetic and Molecular Complexity for in Silico Chemistry. 1237-1243
• 
  Mats G. Gustafsson: Independent Component Analysis Yields Chemically Interpretable Latent Variables in Multivariate Regression. 1244-1255
• 
  Ester Papa, Fulvio Villa, Paola Gramatica: Statistically Validated QSARs, Based on Theoretical Descriptors, for Modeling Aquatic Toxicity of Organic Chemicals in Pimephales promelas (Fathead Minnow). 1256-1266

• 
  Matheus Froeyen, Piet Herdewijn: Correct Bond Order Assignment in a Molecular Framework Using Integer Linear Programming with Application to Molecules Where Only Non-Hydrogen Atom Coordinates Are Available. 1267-1274
• 
  Ludovic Kurunczi, Edward Seclaman, Tudor I. Oprea, Luminita Crisan, Zeno Simon: MTD-PLS: A PLS Variant of the Minimal Topologic Difference Method. III. Mapping Interactions between Estradiol Derivatives and the Alpha Estrogenic Receptor. 1275-1281
• 
  Anna Vulpetti, Patrizia Crivori, Alexander Cameron, Jay Bertrand, Maria Gabriella Brasca, Roberto D'Alessio, Paolo Pevarello: Structure-Based Approaches to Improve Selectivity: CDK2-GSK3beta Binding Site Analysis. 1282-1290
• 
  Iris Antes, Christian Merkwirth, Thomas Lengauer: POEM: Parameter Optimization Using Ensemble Methods: Application to Target Specific Scoring Functions. 1291-1302
• 
  Duangkamol Tantanak, Jumras Limtrakul, Matthew Paul Gleeson: Probing the Structural and Electronic Factors Affecting the Adsorption and Reactivity of Alkenes in Acidic Zeolites Using DFT Calculations and Multivariate Statistical Methods. 1303-1312
• 
  Marie M. Ahlström, Marianne Ridderström, Kristina Luthman, Ismael Zamora: Virtual Screening and Scaffold Hopping Based on GRID Molecular Interaction Fields. 1313-1323

• 
  Nicole A. Kratochwil, Pari Malherbe, Lothar Lindemann, Martin Ebeling, Marius C. Hoener, Andreas Mühlemann, Richard H. P. Porter, Martin Stahl, Paul R. Gerber: An Automated System for the Analysis of G Protein-Coupled Receptor Transmembrane Binding Pockets: Alignment, Receptor-Based Pharmacophores, and Their Application. 1324-1336

• 
  Ron Jones, Paul C. Connolly, Andreas Klamt, Michael Diedenhofen: Use of Surface Charges from DFT Calculations To Predict Intestinal Absorption. 1337-1342
• 
  Hsin-Yuan Wei, Keng-Chang Tsai, Thy-Hou Lin: Modeling Ligand-Receptor Interaction for Some MHC Class II HLA-DR4 Peptide Mimetic Inhibitors Using Several Molecular Docking and 3D QSAR Techniques. 1343-1351
• 
  Kunal Roy, J. Thomas Leonard: QSAR Analyses of 3-(4-Benzylpiperidin-1-yl)-N-phenylpropylamine Derivatives as Potent CCR5 Antagonists. 1352-1368
• 
  Andreas Bender, Robert C. Glen: A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication. 1369-1375
• 
  Hu Li, Chun Wei Yap, Choong Yong Ung, Ying Xue, Zhi Wei Cao, Yu Zong Chen: Effect of Selection of Molecular Descriptors on the Prediction of Blood-Brain Barrier Penetrating and Nonpenetrating Agents by Statistical Learning Methods. 1376-1384
• 
  Brian W. Clare, Claudiu T. Supuran: Predictive Flip Regression: A Technique for QSAR of Derivatives of Symmetric Molecules. 1385-1391

• 
  Yun Xu, Richard G. Brereton: Diagnostic Pattern Recognition on Gene-Expression Profile Data by Using One-Class Classification. 1392-1401
• 
  Joel R. Bock, David A. Gough: Virtual Screen for Ligands of Orphan G Protein-Coupled Receptors. 1402-1414
• 
  Channa K. Hattotuwagama, Irini A. Doytchinova, Darren R. Flower: In Silico Prediction of Peptide Binding Affinity to Class I Mouse Major Histocompatibility Complexes: A Comparative Molecular Similarity Index Analysis (CoMSIA) Study. 1415-1423
• 
  Zheng Rong Yang, Felicia Charles Johnson: Prediction of T-Cell Epitopes Using Biosupport Vector Machines. 1424-1428
• 
  Daniele Dell'Orco, Michele Seeber, Pier Giuseppe De Benedetti, Francesca Fanelli: Probing Fragment Complementation by Rigid-Body Docking: in Silico Reconstitution of Calbindin D9k. 1429-1438

• 
  Ralph T. Mosley, J. Christopher Culberson, Bryan Kraker, Bradley P. Feuston, Robert P. Sheridan, John F. Conway, Joseph K. Forbes, Subhas J. Chakravorty, Simon K. Kearsley: Reagent Selector: Using Synthon Analysis to Visualize Reagent Properties and Assist in Combinatorial Library Design. 1439-1446
• 
  Rafal Gieleciak, Tomasz Magdziarz, Andrzej Bak, Jaroslaw Polanski: Modeling Robust QSAR. 1. Coding Molecules in 3D-QSAR - from a Point to Surface Sectors and Molecular Volumes. 1447-1455
• 
  Frank Oellien, Wolf-Dietrich Ihlenfeldt, Johann Gasteiger: InfVis - Platform-Independent Visual Data Mining of Multidimensional Chemical Data Sets. 1456-1467

• 
  John J. Irwin: Software Review: ChemOffice 2005 Pro by CambridgeSoft. 1468-1469
• 
  Dana L. Roth: SPRESIweb 2.1, a Selective Chemical Synthesis and Reaction Database. 1470-1473
• 
  Achim Zielesny: Chemistry Software Package ChemOffice Ultra 2005. 1474-1477

Volume 45, Number 6, November 2005

• 
  Dusanka Janezic: The Regional Biophysics Meeting March 16-20, 2005, Zrece, Slovenia. 1481
• 
  Volkmar Heinrich, Andrew Leung, Evan Evans: Nano-to-Microscale Mechanical Switches and Fuses Mediate Adhesive Contacts between Leukocytes and the Endothelium. 1482-1490
• 
  Vlado Malacic, Patricija Mozetic: Modeling of the Spread of an Effluent and the Overturning Length Scale near an Underwater Source in the Northern Adriatic. 1491-1501
• 
  Joachim Scholz-Starke, Alessia Naso, Armando Carpaneto: A Perspective on the Slow Vacuolar Channel in Vacuoles from Higher Plant Cells. 1502-1506

• 
  Federico Marini, Alessandra Roncaglioni, Marjana Novic: Variable Selection and Interpretation in Structure-Affinity Correlation Modeling of Estrogen Receptor Binders. 1507-1519
• 
  Katalin Tenger, Petro Khoroshyy, Balázs Leitgeb, Gábor Rákhely, Natalia Borovok, Alexander Kotlyar, Dmitry A. Dolgikh, László Zimányi: Complex Kinetics of the Electron Transfer between the Photoactive Redox Label TUPS and the Heme of Cytochrome c. 1520-1526
• 
  Klavdija Kutnar, Aleksander Malnic, Dragan Marusic: Chirality of Toroidal Molecular Graphs. 1527-1535
• 
  Pavle R. Andjus, Aleksandar Bajic, Lan Zhu, Piergiorgio Strata: Metabotropic Glutamate Receptor-Mediated Currents at the Climbing Fiber to Purkinje Cell Synapse. 1536-1538
• 
  Mauro Dalla Serra, Manuela Coraiola, Gabriella Viero, Massimiliano Comai, Cristina Potrich, Mercedes Ferreras, Lamine Baba-Moussa, Didier A. Colin, Gianfranco Menestrina, Sucharit Bhakdi, Gilles Prévost: Staphylococcus aureus Bicomponent gamma-Hemolysins, HlgA, HlgB, and HlgC, Can Form Mixed Pores Containing All Components. 1539-1545
• 
  Urban Bren, Milan Hodoscek, Joze Koller: Development and Validation of Empirical Force Field Parameters for Netropsin. 1546-1552
• 
  Magdy Lucic Lavcevic, Pavo Dubcek, Zorica Crnjak Orel, Aleksandra Turkovic: GISAXS View of Vanadium/Cerium Oxide Thin Films and Influence of Lithium Intercalation. 1553-1557
• 
  Marjan Sterk, Roman Trobec: Biomedical Simulation of Heat Transfer in a Human Heart. 1558-1563
• 
  Philippe Huetz, Nasim Mavaddat, Janez Mavri: Reaction between Ellagic Acid and an Ultimate Carcinogen. 1564-1570
• 
  Matej Praprotnik, Dusanka Janezic: Molecular Dynamics Integration Meets Standard Theory of Molecular Vibrations. 1571-1579
• 
  Marilena Di Valentin, Arianna Bisol, Giancarlo Agostini, Donatella Carbonera: Electronic Coupling Effects on Photoinduced Electron Transfer in Carotene-Porphyrin-Fullerene Triads Detected by Time-Resolved EPR. 1580-1588
• 
  David Halozan, Christophe Déjugnat, Milan Brumen, Gleb B. Sukhorukov: Entrapment of a Weak Polyanion and H⁺/Na⁺ Exchange in Confined Polyelectrolyte Microcapsules. 1589-1592
• 
  Franci Merzel, Jeremy C. Smith: High-Density Hydration Layer of Lysozymes: Molecular Dynamics Decomposition of Solution Scattering Data. 1593-1599
• 
  Urban Borstnik, Dusanka Janezic: Symplectic Molecular Dynamics Simulations on Specially Designed Parallel Computers. 1600-1604
• 
  Ales Fajmut, Marko Jagodic, Milan Brumen: Mathematical Modeling of the Myosin Light Chain Kinase Activation. 1605-1609
• 
  Ales Fajmut, Andrej Dobovisek, Milan Brumen: Mathematical Modeling of the Relation between Myosin Phosphorylation and Stress Development in Smooth Muscles. 1610-1615
• 
  Dubravka Krilov, Janko N. Herak: Probabilistic Kinetic Model of Slow Oxidation of Low-Density Lipoprotein. 3. Hydroperoxide-Free Initiation. 1616-1620
• 
  David Stopar, Janez Strancar, Ruud B. Spruijt, Marcus A. Hemminga: Exploring the Local Conformational Space of a Membrane Protein by Site-Directed Spin Labeling. 1621-1627
• 
  Aleh A. Kavalenka, Bogdan Filipic, Marcus A. Hemminga, Janez Strancar: Speeding Up a Genetic Algorithm for EPR-Based Spin Label Characterization of Biosystem Complexity. 1628-1635
• 
  Marija Raguz, Jasminka Brnjas-Kraljevic: Resolved Fluorescence Emission Spectra of PRODAN in Ethanol/Buffer Solvents. 1636-1640
• 
  Árpád Karsai, Attila Nagy, András Kengyel, Zsolt Mártonfalvi, László Grama, Botondtól Penke, Miklós S. Z. Kellermayer: Effect of Lysine-28 Side-Chain Acetylation on the Nanomechanical Behavior of Alzheimer Amyloid beta25-35 Fibrils. 1641-1646
• 
  Igor Weber: Receptor Occupancy on an Ellipsoidal Cell in the Presence of a Point Source of a Chemoattractant. 1647-1651
• 
  Miha Fosnaric, Klemen Bohinc, Dorit R. Gauger, Ales Iglic, Veronika Kralj-Iglic, Sylvio May: The Influence of Anisotropic Membrane Inclusions on Curvature Elastic Properties of Lipid Membranes. 1652-1661
• 
  Zoran Arsov, Janez Strancar: Determination of Partition Coefficient of Spin Probe between Different Lipid Membrane Phases. 1662-1671
• 
  Andrej Vilfan: Influence of Fluctuations in Actin Structure on Myosin V Step Size. 1672-1675
• 
  Nejc Tomsiè, Blaz Babnik, Darko Lombardo, Blaz Mavcic, Masa Kanduser, Ales Iglic, Veronika Kralj-Iglic: Shape and Size of Giant Unilamellar Phospholipid Vesicles Containing Cardiolipin. 1676-1679
• 
  Ivan Spasojevic, Vuk Maksimovic, Joanna Zakrzewska, Goran Bacic: Effects of 5-Fluorouracil on Erythrocytes in Relation to Its Cardiotoxicity: Membrane Structure and Functioning. 1680-1685
• 
  Igor Sersa, Gregor Tratar, Ales Blinc: Blood Clot Dissolution Dynamics Simulation during Thrombolytic Therapy. 1686-1690
• 
  Anna Segalla, Ildikó Szabó, Paola Costantini, Giorgio Mario Giacometti: Study of the Effect of Ion Channel Modulators on Photosynthetic Oxygen Evolution. 1691-1700
• 
  Tilen Koklic, Mateja Pirs, Reiner Zeisig, Zrinka Abramovic, Marjeta Sentjurc: Membrane Switch Hypothesis. 1. Cell Density Influences Lateral Domain Structure of Tumor Cell Membranes. 1701-1707
• 
  Petra Kramaric, Zlatko Pavlica, Tilen Koklic, Alenka Nemec, Nevenka Kozuh Erzen, Marjeta Sentjurc: Membrane Switch Hypothesis. 2. Domain Structure of Phagocytes in Horses with Recurrent Airway Obstruction. 1708-1715
• 
  Milos Mojovic, Ivan Spasojevic, Goran Bacic: Detection of Hydrogen Atom Adduct of Spin-Trap DEPMPO. The Relevance for Studies of Biological Systems. 1716-1718

• 
  Erwin Lijnen, Arnout Ceulemans: Topology-Aided Molecular Design: The Platonic Molecules of Genera 0 to 3. 1719-1726

• 
  Stephanie E. Harris, A. Guy Orpen, Ian J. Bruno, Robin Taylor: Factors Affecting d-Block Metal-Ligand Bond Lengths: Toward an Automated Library of Molecular Geometry for Metal Complexes. 1727-1748
• 
  Yun-De Xiao, Aaron Clauset, Rebecca Harris, Ersin Bayram, Peter Santago II, Jeffrey D. Schmitt: Supervised Self-Organizing Maps in Drug Discovery. 1. Robust Behavior with Overdetermined Data Sets. 1749-1758
• 
  Alba T. Macias, Md. Younus Mia, Guanjun Xia, Jun Hayashi, Alexander D. MacKerell Jr.: Lead Validation and SAR Development via Chemical Similarity Searching; Application to Compounds Targeting the pY+3 Site of the SH2 Domain of p56^lck. 1759-1766
• 
  Paolo Mazzatorta, Martin Smiesko, Elena Lo Piparo, Emilio Benfenati: QSAR Model for Predicting Pesticide Aquatic Toxicity. 1767-1774
• 
  Qing-You Zhang, João Aires-de-Sousa: Structure-Based Classification of Chemical Reactions without Assignment of Reaction Centers. 1775-1783
• 
  S. Frank Yan, Hayk Asatryan, Jing Li, Yingyao Zhou: Novel Statistical Approach for Primary High-Throughput Screening Hit Selection. 1784-1790
• 
  Ralph A. Mansson, Jeremy G. Frey, Jonathan W. Essex, Alan H. Welsh: Prediction of Properties from Simulations: A Re-examination with Modern Statistical Methods. 1791-1803
• 
  Lei Yang, Peng Wang, Yilin Jiang, Jian Chen: Studying the Explanatory Capacity of Artificial Neural Networks for Understanding Environmental Chemical Quantitative Structure-Activity Relationship Models. 1804-1811
• 
  Jeffrey W. Godden, Florence L. Stahura, Jürgen Bajorath: Anatomy of Fingerprint Search Calculations on Structurally Diverse Sets of Active Compounds. 1812-1819
• 
  Yongliang Yang, Dmitri V. Nesterenko, Ryan P. Trump, Ken Yamaguchi, Paul A. Bartlett, Dale G. Drueckhammer: Virtual Hydrocarbon and Combinatorial Databases for Use with CAVEAT. 1820-1823
• 
  Justin Klekota, Erik Brauner, Stuart L. Schreiber: Identifying Biologically Active Compound Classes Using Phenotypic Screening Data and Sampling Statistics. 1824-1836

• 
  Tadeusz Marek Krygowski, Joanna E. Zachara, Robert Moszynski: Theoretical Study of Changes in pi-Electron Delocalization in the Analogues of an ortho-Hydroxy Schiff Base When the Proton Is Replaced with Li⁺ or BeH⁺. 1837-1841
• 
  Artem Cherkasov, Zheng Shi, Yvonne Y. Li, Steven J. M. Jones, Magid Fallahi, Geoffrey L. Hammond: 'Inductive' Charges on Atoms in Proteins: Comparative Docking with the Extended Steroid Benchmark Set and Discovery of a Novel SHBG Ligand. 1842-1853
• 
  Kaushal Rege, Asif Ladiwala, Shanghui Hu, Curt M. Breneman, Jonathan S. Dordick, Steven M. Cramer: Investigation of DNA-Binding Properties of an Aminoglycoside-Polyamine Library Using Quantitative Structure-Activity Relationship (QSAR) Models. 1854-1863

• 
  Pierre Crettaz, Romualdo Benigni: Prediction of the Rodent Carcinogenicity of 60 Pesticides by the DEREKfW Expert System. 1864-1873

• 
  Samuli-Petrus Korhonen, Kari Tuppurainen, Reino Laatikainen, Mikael Peräkylä: Comparing the Performance of FLUFF-BALL to SEAL-CoMFA with a Large Diverse Estrogen Data Set: From Relevant Superpositions to Solid Predictions. 1874-1883
• 
  Michael Fernández, Alain Tundidor-Camba, Julio Caballero: Modeling of Cyclin-Dependent Kinase Inhibition by 1H-Pyrazolo[3, 4-d]Pyrimidine Derivatives Using Artificial Neural Network Ensembles. 1884-1895
• 
  Nahoum G. Anthony, Guillaume Huchet, Blair F. Johnston, John A. Parkinson, Colin J. Suckling, Roger D. Waigh, Simon P. Mackay: In Silico Footprinting of Ligands Binding to the Minor Groove of DNA. 1896-1907
• 
  Andrew J. S. Knox, Mary J. Meegan, Giorgio Carta, David G. Lloyd: Considerations in Compound Database Preparation-"Hidden" Impact on Virtual Screening Results. 1908-1919
• 
  Jianfeng Pei, Hao Chen, Zhenming Liu, Xiaofeng Han, Qi Wang, Bin Shen, Jiaju Zhou, Luhua Lai: Improving the Quality of 3D-QSAR by Using Flexible-Ligand Receptor Models. 1920-1933
• 
  Madhu Chopra, Anil K. Mishra: Ligand-Based Molecular Modeling Study on a Chemically Diverse Series of Cholecystokinin-B/Gastrin Receptor Antagonists: Generation of Predictive Model. 1934-1942

• 
  Konstantin B. Tarmyshov, Florian Müller-Plathe: Parallelizing a Molecular Dynamics Algorithm on a Multiprocessor Workstation Using OpenMP. 1943-1952
• 
  Mikko J. Vainio, Mark S. Johnson: McQSAR: A Multiconformational Quantitative Structure-Activity Relationship Engine Driven by Genetic Algorithms. 1953-1961

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