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Protein flexibility in docking and surface mapping

Published online by Cambridge University Press:  09 May 2012

Katrina W. Lexa  and
Heather A. Carlson
Katrina W. Lexa
Affiliation:
Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, MI 48109-1065, USA
Heather A. Carlson*
Affiliation:
Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, MI 48109-1065, USA
*
*Author for correspondence: Heather A. Carlson. Email: [email protected]
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Abstract

Structure-based drug design has become an essential tool for rapid lead discovery and optimization. As available structural information has increased, researchers have become increasingly aware of the importance of protein flexibility for accurate description of the native state. Typical protein–ligand docking efforts still rely on a single rigid receptor, which is an incomplete representation of potential binding conformations of the protein. These rigid docking efforts typically show the best performance rates between 50 and 75%, while fully flexible docking methods can enhance pose prediction up to 80–95%. This review examines the current toolbox for flexible protein–ligand docking and receptor surface mapping. Present limitations and possibilities for future development are discussed.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 45 , Issue 3 , August 2012 , pp. 301 - 343
Copyright
Copyright © Cambridge University Press 2012

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