3D QSAR in Drug Design

1. Front Matter

   Pages i-ix

   PDF

2. 3D QSAR Methodology CoMFA and Related Approaches

   1. 3D QSAR: Current State, Scope, and Limitations

      • Yvonne Connolly Martin

      Pages 3-23

   2. Recent Progress in CoMFA Methodology and Related Techniques

      • Ulf Norinder

      Pages 25-39

   3. Improving the Predictive Quality of CoMFA Models

      • Romano T. Kroemer, Peter Hecht, Stefan Guessregen, Klaus R. Liedl

      Pages 41-56

   4. Cross-Validated R² Guided Region Selection for CoMFA Studies

      • Alexander Tropsha, Sung Jin Cho

      Pages 57-69

   5. GOLPE-Guided Region Selection

      • Gabriele Cruciani, Sergio Clementi, Manuel Pastor

      Pages 71-86

   6. Comparative Molecular Similarity Indices Analysis: CoMSIA

      • Gerhard Klebe

      Pages 87-104

   7. Alternative Partial Least-Squares (PLS) Algorithms

      • Fredrik Lindgren, Stefan Rännar

      Pages 105-113

3. Receptor Models and Other 3D QSAR Approaches

   1. Receptor Surface Models

      • Mathew Hahn, David Rogers

      Pages 117-133

   2. Pseudoreceptor Modelling in Drug Design: Applications of Yak and PrGen

      • Marion Gurrath, Gerhard Müller, Hans-Dieter Höltje

      Pages 135-157

   3. Genetically Evolved Receptor Models (GERM) as a 3D QSAR Tool

      • D. Eric Walters

      Pages 159-166

   4. 3D QSAR of Flexible Molecules Using Tensor Representation

      • William J. Dunn III, Antony J. Hopfinger

      Pages 167-182

   5. Comparative Molecular Moment Analysis (CoMMA)

      • B. David Silverman, Daniel E. Platt, Mike Pitman, Isidore Rigoutsos

      Pages 183-196

4. 3D QSAR Applications

   1. The CoMFA Steroids as a Benchmark Dataset for Development of 3D QSAR Methods

      • Eugene A. Coats

      Pages 199-213

   2. Molecular Similarity Characterization Using CoMFA

      • Thierry Langer

      Pages 215-231

   3. Building a Bridge between G-Protein-Coupled Receptor Modelling, Protein Crystallography and 3D QSAR Studies for Ligand Design

      • Ki Hwan Kim

      Pages 233-255

   4. A Critical Review of Recent CoMFA Applications

      • Ki Hwan Kim, Giovanni Greco, Ettore Novellino

      Pages 257-315

5. Back Matter

   Pages 317-353

   PDF

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.

• algorithms
• biological
• crystal
• crystallography
• development
• dynamics
• energy
• experiment
• fields
• mechanics
• molecule
• protein
• quality
• receptor
• silver

`... 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

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

  Yvonne C. Martin

Policies and ethics