Chapter I-8. Modelling Protein–Protein and Protein–DNA Docking

  1. Prof. Dr. Thomas Lengauer Ph.D.
  1. Dr. Michael J. E. Sternberg and
  2. Dr. Gidon Moont

Published Online: 1 APR 2004

DOI: 10.1002/3527601481.ch8

Bioinformatics ‐ From Genomes to Drugs

Bioinformatics - From Genomes to Drugs

How to Cite

Sternberg, M. J. E. and Moont, G. (2001) Modelling Protein–Protein and Protein–DNA Docking, in Bioinformatics - From Genomes to Drugs (ed T. Lengauer), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG. doi: 10.1002/3527601481.ch8

Editor Information

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

Author Information

  1. Imperial Cancer Research Fund, Biomolecular Modelling Laboratory, 44 Lincoln's Inn Fields, London WC2A 3PX, United Kingdom

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–protein docking;
  • protein–DNA docking;
  • protein complexes;
  • Fourier correlation theory;
  • re-rank putative docked complexes


This chapter contains sections titled:

  • Introduction

    • The need for protein–protein and protein–DNA docking

    • Overview of the computational approach

    • Scope of this chapter

  • Structural studies of protein complexes

  • Methodology of a protein–protein docking strategy

    • Rigid body docking by Fourier correlation theory

    • Use of residue pair potentials to re-rank docked complexes

    • Use of distance constraints

    • Refinement and additional screening of complexes

    • Implementation of the docking suite

  • Results from the protein–protein docking strategy

  • Modelling protein–DNA complexes

    • Method

    • Results

  • Strategies for protein–protein docking

    • Evaluation of the results of docking simulations

    • Fourier correlation methods

    • Other rigid-body docking approaches

    • Flexible protein–protein docking

    • Rigid-body treatment to re-rank putative docked complexes

    • Introduction of flexibility to re-rank putative docked complexes

  • Blind trials of protein–protein docking

  • Energy landscape for protein docking

  • Conclusions