Chemoinformatics : concepts, methods, and tools for drug discovery

Preface .............................................................................................................v Contributors ..................................................................................................... xi 1 Molecular Similarity Measures Gerald M. Maggiora and Veerabahu Shanmugasundaram .............. 1 2 Evaluation of Molecular Similarity and Molecular Diversity Methods Using Biological Activity Data Peter Willett .......................................................................................... 51 3 A Web-Based Chemoinformatics System for Drug Discovery Scott D. Bembenek, Brett A. Tounge, Steven J. Coats, and Charles H. Reynolds ................................................................ 65 4 Application of Chemoinformatics to High Throughput Screening: Practical Considerations Christian N. Parker and Suzanne K. Schreyer ................................. 85 5 Strategies for the Identification and Generation of Informative Compound Sets Michael S. Lajiness and Veerabahu Shanmugasundaram ........... 111 6 Methods for Applying the Quantitative Structure–Activity Relationship Paradigm Emilio Xavier Esposito, Anton J. Hopfinger, and Jeffry D. Madura ..................................................................... 131 7 3D-LogP: An Alignment-Free 3D Description of Local Lipophilicity for QSAR Studies Jérôme Gomar, Elie Giraud, David Turner, Roger Lahana, and Pierre Alain Carrupt ............................................................... 215 8 Derivation and Applications of Molecular Descriptors Based on Approximate Surface Area Paul Labute ......................................................................................... 261 9 Cell-Based Partitioning Ling Xue, Florence L. Stahura, and Jürgen Bajorath ................... 279 10 Partitioning in Binary-Transformed Chemical Descriptor Spaces Jeffrey W. Godden and Jürgen Bajorath ........................................ 291 ix x Contents 11 Comparison of Methods Based on Diversity and Similarity for Molecule Selection and the Analysis of Drug Discovery Data Raymond L. H. Lam and William J. Welch...................................... 301 12 Using Recursive Partitioning Analysis to Evaluate Compound Selection Methods S. Stanley Young and Douglas M. Hawkins.................................... 317 13 Designing Combinatorial Libraries Optimized on Multiple Objectives Valerie J. Gillet ................................................................................... 335 14 Approaches to Target Class Combinatorial Library Design Dora Schnur, Brett R. Beno, Andrew Good, and Andrew Tebben ...................................................................... 355 15 Simulated Annealing: An Effective Stochastic Optimization Approach to Computational Library Design Weifan Zheng ..................................................................................... 379 16 Genetic Algorithms for Classification of Olfactory Stimulants Barry K. Lavine, Charles E. Davidson, Curt Breneman, and William Kaat ............................................................................ 399 17 How to Describe Chirality and Conformational Flexibility Gordon M. Crippen ............................................................................ 427 18 Novel Scoring Methods in Virtual Ligand Screening Daniel Pick .......................................................................................... 439 19 Prediction of Drug-like Molecular Properties: Modeling Cytochrome P450 Interactions Mehran Jalaie, Rieko Arimoto, Eric Gifford, Sabine Schefzick, and Chris L. Waller ....................................... 449 Index ............................................................................................................ 521