14. Embracing Protein Plasticity in Ligand Docking

  1. Prof. Dr. Holger Gohlke
  1. Manuel Rueda1 and
  2. Ruben Abagyan1,2,3

Published Online: 20 APR 2012

DOI: 10.1002/9783527645947.ch14

Protein-Ligand Interactions, First Edition

Protein-Ligand Interactions, First Edition

How to Cite

Rueda, M. and Abagyan, R. (2012) Embracing Protein Plasticity in Ligand Docking, in Protein-Ligand Interactions, First Edition (ed H. Gohlke), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527645947.ch14

Editor Information

  1. Heinrich-Heine-Universität, Inst.für Pharmaz. + Med.Chemie, Universitätsstr. 1, 40225 Düsseldorf, Germany

Author Information

  1. 1

    University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA

  2. 2

    University of California, San Diego, San Diego Supercomputer Center, La Jolla, CA 92093, USA

  3. 3

    Molsoft LLC, 11199 Sorrento Valley Road, S209, San Diego, CA 92121, USA

Publication History

  1. Published Online: 20 APR 2012
  2. Published Print: 18 APR 2012

Book Series:

  1. Methods and Principles in Medicinal Chemistry

Book Series Editors:

  1. Prof. Dr. Raimund Mannhold5,
  2. Prof. Dr. Hugo Kubinyi6 and
  3. Prof. Dr. Gerd Folkers7

Series Editor Information

  1. 5

    Molecular Drug Research Group, Heinrich-Heine-Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany

  2. 6

    Donnersbergstrasse 9, 67256 Weisenheim am Sand, Germany

  3. 7

    Collegium Helveticum, STW/ETH Zurich, 8092 Zurich, Switzerland

ISBN Information

Print ISBN: 9783527329663

Online ISBN: 9783527645947

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Keywords:

  • binding pocket;
  • docking;
  • drug design;
  • plasticity;
  • receptor conformation;
  • virtual ligand screening

Summary

This chapter contains sections titled:

  • Introduction

  • Docking by Sampling Internal Coordinates

  • Fast Docking to Multiple Receptor Conformations

  • Single Receptor Conformation

  • Multiple Receptor Conformations

  • Improving Poor Homology Models of the Binding Pocket

  • State of the Art: GPCR Dock 2010 Modeling and Docking Assessment

  • Conclusions and Outlook

  • Acknowledgments

  • References