3D QSAR in Drug Design Recent Advances
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
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QSAR = Three-Dimensional Quantitative Structure Activity Relationships VOLUME 3
The titles published in this series are listed at the end of this volume.
3D QSAR in Drug Design Volume 3 Recent Advances
Edited by
Hugo Kubinyi ZHF/G, A30, BASF AG, D-67056 Ludwigshafen, Germany
Gerd Folkers ETH-Zürich, Department Pharmazie, Winterthurer Strasse 190, CH-8057 Zürich, Switzerland
Yvonne C. Martin Abbott Laboratories, Pharmaceutical Products Division, 100 Abbott Park Rd., Abbott Park, IL 60064-3500, USA
KLUWER ACADEMIC PUBLISHERS NEW YORK, BOSTON, DORDRECHT, LONDON, MOSCOW
eBook ISBN: Print ISBN:
0-306-46858-1 0-7923-4791-9
©2002 Kluwer Academic Publishers New York, Boston, Dordrecht, London, Moscow Print ©1998 KLUWER/ESCOM Dordrecht All rights reserved
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Contents
Preface
vii
Part I. 3D QSAR Methodology. CoMFA and Related Approaches 3D QSAR: Current State, Scope, and Limitations Yvonne Connolly Martin
3
Recent Progress in CoMFA Methodology and Related Techniques UlfNorinder
25
Improving the Predictive Quality of CoMFA Models Romano T. Kroemer, Peter Hecht, Stefan Guessregen and Klaus R. Liedl
41
Cross-Validated Guided Region Selection for CoMFA Studies Alexander Tropsha and Sung Jin Cho
57
GOLPE-Guided Region Selection
71
Gabriele Cruciani, Sergio dementi and Manuel Pastor Comparative Molecular Similarity Indices Analysis: CoMSIA Gerhard Klebe Alternative Partial Least Squares (PLS) Algorithms Fredrik Lindgren and Stefan Rännar
87
105
Part II. Receptor Models and Other 3D QSAR Approaches Receptor Surface Models Mathew Hahn and David Rogers
117
Pseudoreceptor Modelling in Drug Design: Applications of Yak and PrGen Marion Gurrath, Gerhard Müller and Hans-Dieter Höltje
135
Genetically Evolved Receptor Models (GERM) as a 3D QSAR Tool D. Eric Walters
159
3D QSAR of Flexible Molecules Using Tensor Representation William J. Dunn and Antony J. Hopfinger
167
v
Contents
Comparative Molecular Moment Analysis (CoMMA) B. David Silverman, Daniel E. Plan, Mike Pitman and Isidore Rigoutsos
183
Part III. 3D QSAR Applications The CoMFA Steroids as a Benchmark Dataset for Development of 3D QSAR Methods Eugene A. Coats
199
Molecular Similarity Characterization using CoMFA Thierry Langer
215
Building a Bridge between G-Protein-Coupled Receptor Modelling, Protein Crystallography and 3D QSAR Studies for Ligand Design Ki Hwan Kim
233
A Critical Review of Recent CoMFA Applications Ki Hwan Kim, Giovanni Greco and Ettore Novellino
257
List of CoMFA References, 1993-1996
317
List of COMFA References, 1997 Ki Hwan Kim
334
Author Index
339
Subject Index
341
vi
Preface
Significant progress has been made in the study of three-dimensional quantitative
structure-activity re
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