3D QSAR in Drug Design

1. Front Matter

   Pages i-x

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2. Ligand-Protein Interactions

   1. Progress in Force-Field Calculations of Molecular Interaction Fields and Intermolecular Interactions

      • Tommy Liljefors

      Pages 3-17

   2. Comparative Binding Energy Analysis

      • Rebecca C. Wade, Angel R. Qrtiz, Federico Gago

      Pages 19-34

   3. Receptor-Based Prediction of Binding Affinities

      • Tudor I. Oprea, Garland R. Marshall

      Pages 35-61

   4. A Priori Prediction of Ligand Affinity by Energy Minimization

      • M. Katharine Holloway

      Pages 63-84

   5. Rapid Estimation of Relative Binding Affinities of Enzyme Inhibitors

      • M. Rami Reddy, Velarkad N. Viswanadhan, M. D. Erion

      Pages 85-98

   6. Binding Affinities and Non-Bonded Interaction Energies

      • Ronald M. A. Knegtel, Peter D. J. Grootenhuis

      Pages 99-114

   7. Molecular Mechanics Calculations on Protein-Ligand Complexes

      • Irene T. Weber, Robert W. Harrison

      Pages 115-127

3. Quantum Chemical Models and Molecular Dynamics Simulations

   1. Some Biological Applications of Semiempirical MO Theory

      • Bernd Beck, Timothy Clark

      Pages 131-159

   2. Density-Functional Theory and Molecular Dynamics: A New Perspective for Simulations of Biological Systems

      • Wanda Andreoni

      Pages 161-167

   3. Density-Functional Theory Investigations of Enzyme-substrate Interactions

      • Paolo Carloni, Frank Alber

      Pages 169-179

   4. Molecular Dynamics Simulations: A Tool for Drug Design

      • Didier Rognan

      Pages 181-209

4. Pharmacophore Modelling and Molecular Similarity

   1. Bioisosterism and Molecular Diversity

      • Robert D. Clark, Allan M. Ferguson, Richard D. Cramer

      Pages 213-224

   2. Similarity and Dissimilarity: A Medicinal Chemist’s View

      • Hugo Kubinyi

      Pages 225-252

   3. Pharmacophore Modelling: Methods,Experimental Verification and Applications

      • Arup K. Ghose, John J. Wendoloski

      Pages 253-271

   4. The Use of Self-organizing Neural Networks in Drug Design

      • Soheila Anzali, Johann Gasteiger, Ulrike Holzgrabe, Jaroslaw Polanski, Jens Sadowski, Andreas Teckentrupb Markus Wagener

      Pages 273-299

   5. Calculation of Structural Similarity by the Alignment of Molecular Electrostatic Potentials

      • David A. Thorner, David J. Wild, Peter Willett, P. Matthew Wright

      Pages 301-320

   6. Explicit Calculation of 3D Molecular Similarity

      • Andrew C. Good, W.Graham Richards

      Pages 321-338

   7. Novel Software Tools for Chemical Diversity

      • Robert S. Pearlman, K. M. Smith

      Pages 339-353

   8. New 3D Molecular Descriptors: The WHIM theory and QSAR Applications

      • Roberto Todeschini, Paola Gramatica

      Pages 355-380

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.

• crystal
• drug
• energy
• molecule
• research
• steroids

`... Volume 3 is a valuable resource text for scientists with a background or serious interest in 3D QSAR who are interested in CoMFA and related methodology. overall this 3 book series is a wonderful reference source for scientists interested 3D QSAR.'
SIM News, 49:4 (1999)

• ZHF/G, A30, BASF AG, Ludwigshafen, Germany

  Hugo Kubinyi

• Department Pharmazie, ETH-Zürich, Zürich, Switzerland

  Gerd Folkers

• Abbott Laboratories, Pharmaceutical Products Division, Abbott Park, USA

  Yvonne C. Martin

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