3D QSAR in Drug Design: Volume 2: Ligand-Protein Interactions and Molecular Similarity (Three-Dimensional Quantitative Structure Activity Relationships)

Significant progress has been made in the study of three-dimensional quantitative structure-activity relationships (3D QSAR) since the first publication by Richard Cramer in 1988 and the first volume in the series. 3D QSAR in Drug Design. Theory, Methods and Applications, published in 1993. The aim of that early book was to contribute to the understanding and the further application of CoMFA and related approaches and to facilitate the appropriate use of these methods. Since then, hundreds of papers have appeared using the quickly developing techniques of both 3D QSAR and computational sciences to study a broad variety of biological problems. Again the editor(s) felt that the time had come to solicit reviews on published and new viewpoints to document the state of the art of 3D QSAR in its broadest definition and to provide visions of where new techniques will emerge or new appli- tions may be found. The intention is not only to highlight new ideas but also to show the shortcomings, inaccuracies, and abuses of the methods. We hope this book will enable others to separate trivial from visionary approaches and me-too methodology from in- vative techniques. These concerns guided our choice of contributors. To our delight, our call for papers elicited a great many manuscripts. Progress in Force-Field Calculations of Molecular Interaction Fields and Intermolecular Interactions....Pages 3-17 Comparative Binding Energy Analysis....Pages 19-34 Receptor-Based Prediction of Binding Affinities....Pages 35-61 A Priori Prediction of Ligand Affinity by Energy Minimization....Pages 63-84 Rapid Estimation of Relative Binding Affinities of Enzyme Inhibitors....Pages 85-98 Binding Affinities and Non-Bonded Interaction Energies....Pages 99-114 Molecular Mechanics Calculations on Protein-Ligand Complexes....Pages 115-127 Some Biological Applications of Semiempirical MO Theory....Pages 131-159 Density-Functional Theory and Molecular Dynamics: A New Perspective for Simulations of Biological Systems....Pages 161-167 Density-Functional Theory Investigations of Enzyme-substrate Interactions....Pages 169-179 Molecular Dynamics Simulations: A Tool for Drug Design....Pages 181-209 Bioisosterism and Molecular Diversity....Pages 213-224 Similarity and Dissimilarity: A Medicinal Chemist’s View....Pages 225-252 Pharmacophore Modelling: Methods,Experimental Verification and Applications....Pages 253-271 The Use of Self-organizing Neural Networks in Drug Design....Pages 273-299 Calculation of Structural Similarity by the Alignment of Molecular Electrostatic Potentials....Pages 301-320 Explicit Calculation of 3D Molecular Similarity....Pages 321-338 Novel Software Tools for Chemical Diversity....Pages 339-353 New 3D Molecular Descriptors: The WHIM theory and QSAR Applications....Pages 355-380 EVA: A Novel Theoretical Descriptor for QSAR Studies....Pages 381-398 Volumes 2 and 3 of the 3D QSAR in Drug Design series aim to review the progress being made in CoMFA and other 3D QSAR approaches since the publication of the highly successful first volume about four years ago. Volume 2 (Ligand-Protein Interactions and Molecular Similarity) divides into three sections dealing with Ligand-Protein Interactions, Quantum Chemical Models and Molecular Dynamics Simulations, and Pharmacophore Modelling and Molecular Similarity, respectively. Volume 3 (Recent Advances) is also divided into three sections, namely 3D QSAR Methodology: CoMFA and Related Approaches, Receptor Models and Other 3D QSAR Approaches, and 3D QSAR Applications. More than seventy distinguished scientists have contributed nearly forty reviews of their work and related research to these two volumes which are of outstanding quality and timeliness. These works present an up-to-date coverage of the latest developments in all fields of 3D QSAR