Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking

Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge...

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Main Authors:	Bastard, Karine, Saladin, Adrien, Prévost, Chantal
Format:	Online
Language:	English
Published:	Molecular Diversity Preservation International (MDPI) 2011
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083708/

id	pubmed-3083708
recordtype	oai_dc
spelling	pubmed-30837082011-05-03 Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking Bastard, Karine Saladin, Adrien Prévost, Chantal Review Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success. Molecular Diversity Preservation International (MDPI) 2011-02-22 /pmc/articles/PMC3083708/ /pubmed/21541061 http://dx.doi.org/10.3390/ijms12021316 Text en © 2011 by the authors; licensee MDPI, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0 This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Bastard, Karine Saladin, Adrien Prévost, Chantal
spellingShingle	Bastard, Karine Saladin, Adrien Prévost, Chantal Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking
author_facet	Bastard, Karine Saladin, Adrien Prévost, Chantal
author_sort	Bastard, Karine
title	Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking
title_short	Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking
title_full	Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking
title_fullStr	Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking
title_full_unstemmed	Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking
title_sort	accounting for large amplitude protein deformation during in silico macromolecular docking
description	Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.
publisher	Molecular Diversity Preservation International (MDPI)
publishDate	2011
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083708/
_version_	1611450879658950656

Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking

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