Chapter I-7. Protein–Ligand Docking in Drug Design

  1. Prof. Dr. Thomas Lengauer Ph.D.
  1. Dr. Matthias Rarey

Published Online: 1 APR 2004

DOI: 10.1002/3527601481.ch7

Bioinformatics - From Genomes to Drugs

Bioinformatics - From Genomes to Drugs

How to Cite

Rarey, M. (2001) Protein–Ligand Docking in Drug Design, in Bioinformatics - From Genomes to Drugs (ed T. Lengauer), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG. doi: 10.1002/3527601481.ch7

Editor Information

  1. Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53754 Sankt Augustin, Germany

Author Information

  1. Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, 53754 Sankt Augustin, Germany

Publication History

  1. Published Online: 1 APR 2004
  2. Published Print: 1 NOV 2001

Book Series:

  1. Methods and Principles in Medicinal Chemistry

Book Series Editors:

  1. Prof. Dr. Raimund Mannhold3,
  2. Prof. Dr. Hugo Kubinyi4 and
  3. Prof. Dr. Gerd Folkers5

Series Editor Information

  1. 3

    Biomedical Research Center, Molecular Drug Research Group, Heinrich-Heine-Universität, Universitätsstraße 1, D-40225 Düsseldorf, Germany

  2. 4

    BASF AG, Ludwigshaften, c/o Donnersbergstrasse g, D-67256 Weisenheim am Sand, Germany

  3. 5

    Department of Applied Biosciences, ETH Zürich, Winterthurer Str. 190, CH-8057 Zürich, Switzerland

ISBN Information

Print ISBN: 9783527299881

Online ISBN: 9783527601486



  • protein–ligand docking;
  • drug design;
  • X-ray structures;
  • software


This chapter contains sections titled:

  • Introduction

    • A taxonomy of docking problems

    • Application scenarios in structure-based drug design

  • Methods for protein–ligand docking

    • Rigid-body docking algorithms

    • Flexible ligand docking algorithms

    • Docking by simulation

    • Docking of combinatorial libraries

    • Scoring protein–ligand complexes

  • Validation studies and applications

    • Reproducing X-ray structures

    • Validated blind predictions

    • Screening small molecule databases

    • Docking of combinatorial libraries

  • Molecular docking in practice

    • Preparing input data

    • Analyzing docking results

    • Choosing the right docking tool

  • Concluding remarks

  • Software accessibility