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Flexible Docking and Design

Flexible Docking and Design Docking and design are the major computational steps toward under­ standing and affecting receptor-ligand interactions. The flexibility of many ligands makes these calculations difficult and requires the devel­ opment and use of special methods. The need for such tools is illus­ trated by two examples: the design of protease inhibitors and the analy­ sis and design of peptide antigens binding to specific MHC receptors. We review the computational concepts that have been extended from rigid-body to flexible docking, as well as the following important strate­ gies for flexible docking and design: (a) Monte Carlo/molecular dynam677 1056-8700/95/0610-0677$05.00 ROSENFELD, V AIDA & DeLISI ics docking, (b) in-site combinatorial search, (c) ligand build-up, and (d) site mapping and fragment assembly. The use of empirical free en­ ergy as a target function is discussed. Due to the rapid development of the methodology, most new methods have been tested on only a limited number of applications and are likely to improve results ob­ tained by more traditional computational or graphic tools. INTRODUCTION A critical factor in virtually all biological processes is the specificity of ligands for larger proteins, such as membrane-bound receptors, or enzymes. Ligands may be flexible; for example, neurotransmitters, in­ hibitors, http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Annual Review of Biophysics Annual Reviews

Flexible Docking and Design

Rosenfeld, R; Vajda, S; DeLisi, C
Annual Review of Biophysics , Volume 24 (1) – Jun 1, 1995
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Publisher
Annual Reviews
Copyright
Copyright 1995 Annual Reviews. All rights reserved
Subject
Review Articles
ISSN
1936-122X
eISSN
1936-1238
DOI
10.1146/annurev.bb.24.060195.003333
pmid
7663131
Publisher site
See Article on Publisher Site

Abstract

Docking and design are the major computational steps toward under­ standing and affecting receptor-ligand interactions. The flexibility of many ligands makes these calculations difficult and requires the devel­ opment and use of special methods. The need for such tools is illus­ trated by two examples: the design of protease inhibitors and the analy­ sis and design of peptide antigens binding to specific MHC receptors. We review the computational concepts that have been extended from rigid-body to flexible docking, as well as the following important strate­ gies for flexible docking and design: (a) Monte Carlo/molecular dynam677 1056-8700/95/0610-0677$05.00 ROSENFELD, V AIDA & DeLISI ics docking, (b) in-site combinatorial search, (c) ligand build-up, and (d) site mapping and fragment assembly. The use of empirical free en­ ergy as a target function is discussed. Due to the rapid development of the methodology, most new methods have been tested on only a limited number of applications and are likely to improve results ob­ tained by more traditional computational or graphic tools. INTRODUCTION A critical factor in virtually all biological processes is the specificity of ligands for larger proteins, such as membrane-bound receptors, or enzymes. Ligands may be flexible; for example, neurotransmitters, in­ hibitors,

Journal

Annual Review of Biophysics – Annual Reviews

Published: Jun 1, 1995

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