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Summary

Written by experienced experts in the field, this book describes the basics to the extent necessary for reliably judging the results from molecular modeling calculations. Without unnecessary overhead, it leads readers from simple calculations on small molecules to the modeling of proteins and other relevant biomolecules. Beginners are guided through their first modeling experiment, while routine users of modeling software are provided with invaluable troubleshooting hints. A unique resource for students, researchers and lecturers, now available in this all-new, enlarged edition. "If the currently popular 'Dummies' series of computer books were to publish a volume on molecular modeling this would be it" (Journal of the American Chemical Society) "The book is well written and assumes no prior knowledge of molecular biology, statistical mechanics, or quantum chemistry. The authors provide practical hints for the application of the majority of available programs in computational chemistry" (Computers in Physics)

Author Biography

<b>Hans-Dieter H&#246;ltje</b> is director of the Institute of Pharmaceutical Chemistry at the Heinrich-Heine-Universit&#228;t D&#252;sseldorf, where he also holds the chair of Medicinal Chemistry. His main interest is the molecular mechanism of drug action. He is especially interested in modeling G-Protein-Coupled receptors, cytochromes, enzymes of therapeutic importance and phospholipid membranes. <p> <b>Wolfgang Sippl</b> is Professor of Pharmaceutical Chemistry at the Martin-Luther-University of Halle-Wittenberg, Germany. He is interested in 3<sup>D</sup> QSAR, molecular docking and molecular dynamics, and their applications in drug design and pharmacokinetics. <p> <b>Didier Rognan</b> leads the Drug Bioinformatics Group at the Laboratory for Molecular Pharmacochemistry in Illkrich (France) He is mainly interested in all aspects (method development, applications) of protein-based drug design and virtual screening. <p> <b>Gerd Folkers</b> is Professor of Pharmaceutical Chemistry at the ETH Zurich. The focus of his research is the molecular interaction between drugs and their binding sites. Besides his work on the molecular mechanism of "conventional" nucleoside therapeutics against virus infection and cancer, his special interest has shifted to immuno-therapeutics.

Table of Contents

Introduction
MODELING OF SMALL MOLECULES
Generation of 3 D coordinates
Computational tools for geometry optimizations
Conformational analysis
Determination of molecular interaction potentials
A Case study for small molecule modeling
INTRODUCTION TO PROTEIN MODELING
Principles of protein structure
Comparative protein modeling
Model refinement and molecular dynamics
Validation of protein models
Modeling protein properties
Protein-based virtual screening
Docking Algorithms
Scoring Functions
Virtual Screening
Worked example for the modeling of a protein-ligand complex

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