3D QSAR in Drug Design, Volume 2 also available as Volumes 9-11 (1997) and Volume 3 as Volumes 12-14 (1998) of PERSPECTIVES IN DRUG DISCOVERY AND DESIGN, 1998 Ligand-Protein Interactions and Molecular Similarity Three-Dimensional Quantitative Structure Activity Relationships Series, Vol. 2

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.

Ligand-Protein Interactions.- Progress in Force-Field Calculations of Molecular Interaction Fields and Intermolecular Interactions.- Comparative Binding Energy Analysis.- Receptor-Based Prediction of Binding Affinities.- A Priori Prediction of Ligand Affinity by Energy Minimization.- Rapid Estimation of Relative Binding Affinities of Enzyme Inhibitors.- Binding Affinities and Non-Bonded Interaction Energies.- Molecular Mechanics Calculations on Protein-Ligand Complexes.- Quantum Chemical Models and Molecular Dynamics Simulations.- Some Biological Applications of Semiempirical MO Theory.- Density-Functional Theory and Molecular Dynamics: A New Perspective for Simulations of Biological Systems.- Density-Functional Theory Investigations of Enzyme-substrate Interactions.- Molecular Dynamics Simulations: A Tool for Drug Design.- Pharmacophore Modelling and Molecular Similarity.- Bioisosterism and Molecular Diversity.- Similarity and Dissimilarity: A Medicinal Chemist’s View.- Pharmacophore Modelling: Methods,Experimental Verification and Applications.- The Use of Self-organizing Neural Networks in Drug Design.- Calculation of Structural Similarity by the Alignment of Molecular Electrostatic Potentials.- Explicit Calculation of 3D Molecular Similarity.- Novel Software Tools for Chemical Diversity.- New 3D Molecular Descriptors: The WHIM theory and QSAR Applications.- EVA: A Novel Theoretical Descriptor for QSAR Studies.

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 vo