Modeling Protein-Protein Interactions by Rigid-Body Docking
Identifieur interne : 003274 ( Hal/Curation ); précédent : 003273; suivant : 003275Modeling Protein-Protein Interactions by Rigid-Body Docking
Auteurs : David Ritchie [France]Source :
Abstract
Protein-protein interactions and the formation of protein-protein complexes are central to many biological processes. Protein docking is the task of calculating the three-dimensional structure of a protein complex starting from the individual structures of the constituent proteins. Although proteins are intrinsically flexible, most docking algorithms begin by assuming that the proteins to be docked are rigid. This assumption allows fast rigid-body docking techniques to be used to generate a relatively small list of candidate docking poses which may subsequently be refined using more computationally intensive force-field based approaches. Protein docking predictions are helping to provide a better physical picture of protein-protein interactions, and the use of protein docking is becoming an increasingly important way to help identify potential drug targets. This chapter gives an overview of current theory and practice in the use of computational and data-based protein docking techniques, with particular focus on using fast Fourier transform techniques and modern graphics processors to accelerate the rigid body part of a docking calculation.
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DOI: 10.1039/9781849733403
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Protein docking is the task of calculating the three-dimensional structure of a protein complex starting from the individual structures of the constituent proteins. Although proteins are intrinsically flexible, most docking algorithms begin by assuming that the proteins to be docked are rigid. This assumption allows fast rigid-body docking techniques to be used to generate a relatively small list of candidate docking poses which may subsequently be refined using more computationally intensive force-field based approaches. Protein docking predictions are helping to provide a better physical picture of protein-protein interactions, and the use of protein docking is becoming an increasingly important way to help identify potential drug targets. This chapter gives an overview of current theory and practice in the use of computational and data-based protein docking techniques, with particular focus on using fast Fourier transform techniques and modern graphics processors to accelerate the rigid body part of a docking calculation.</div></front></TEI><hal api="V3"><titleStmt><title xml:lang="en">Modeling Protein-Protein Interactions by Rigid-Body Docking</title><author role="aut"><persName><forename type="first">David</forename><surname>Ritchie</surname></persName><email>Dave.Ritchie@inria.fr</email><ptr type="url" target="http://www.loria.fr/~ritchied/"></ptr><idno type="idhal">david-ritchie</idno><idno type="halauthor">659214</idno><affiliation ref="#struct-205125"></affiliation></author><editor role="depositor"><persName><forename>David</forename><surname>Ritchie</surname></persName><email>Dave.Ritchie@inria.fr</email></editor></titleStmt><editionStmt><edition n="v1" type="current"><date type="whenSubmitted">2012-02-06 12:44:43</date><date type="whenModified">2015-09-22 01:12:59</date><date type="whenReleased">2012-02-06 12:44:43</date><date type="whenProduced">2012</date></edition><respStmt><resp>contributor</resp><name key="145516"><persName><forename>David</forename><surname>Ritchie</surname></persName><email>Dave.Ritchie@inria.fr</email></name></respStmt></editionStmt><publicationStmt><distributor>CCSD</distributor><idno type="halId">hal-00666809</idno><idno type="halUri">https://hal.inria.fr/hal-00666809</idno><idno type="halBibtex">ritchie:hal-00666809</idno><idno type="halRefHtml">Timothy Clark and Lee Banting. Drug Design Strategies: Computational Techniques and Applications, RSC Publishing, pp.56-86, 2012, RSC Drug Discovery Series, 978-1-84973-167-6. <10.1039/9781849733403></idno><idno type="halRef">Timothy Clark and Lee Banting. Drug Design Strategies: Computational Techniques and Applications, RSC Publishing, pp.56-86, 2012, RSC Drug Discovery Series, 978-1-84973-167-6. <10.1039/9781849733403></idno></publicationStmt><seriesStmt><idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno><idno type="stamp" n="INRIA">INRIA - Institut National de Recherche en Informatique et en Automatique</idno><idno type="stamp" n="LORIA2">Publications du LORIA</idno><idno type="stamp" n="INRIA-NANCY-GRAND-EST">INRIA Nancy - Grand Est</idno><idno type="stamp" n="LORIA">LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications</idno><idno type="stamp" n="LORIA-TALC" p="LORIA">Traitement automatique des langues et des connaissances</idno><idno type="stamp" n="INRIA-LORRAINE">INRIA Nancy - Grand Est</idno><idno type="stamp" n="UNIV-LORRAINE">Université de Lorraine</idno><idno type="stamp" n="INRIA_TEST">INRIA - Institut National de Recherche en Informatique et en Automatique</idno></seriesStmt><notesStmt><note type="audience" n="2">International</note><note type="popular" n="0">No</note></notesStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Modeling Protein-Protein Interactions by Rigid-Body Docking</title><author role="aut"><persName><forename type="first">David</forename><surname>Ritchie</surname></persName><email>Dave.Ritchie@inria.fr</email><ptr type="url" target="http://www.loria.fr/~ritchied/"></ptr><idno type="idHal">david-ritchie</idno><idno type="halAuthorId">659214</idno><affiliation ref="#struct-205125"></affiliation></author></analytic><monogr><idno type="isbn">978-1-84973-167-6</idno><title level="m">Drug Design Strategies: Computational Techniques and Applications</title><editor>Timothy Clark and Lee Banting</editor><imprint><publisher>RSC Publishing</publisher><biblScope unit="serie">RSC Drug Discovery Series</biblScope><biblScope unit="pp">56-86</biblScope><date type="datePub">2012</date></imprint></monogr><idno type="doi">10.1039/9781849733403</idno></biblStruct></sourceDesc><profileDesc><langUsage><language ident="en">English</language></langUsage><textClass><classCode scheme="halDomain" n="chim.chem">Chemical Sciences/Cheminformatics</classCode><classCode scheme="halDomain" n="chim.theo">Chemical Sciences/Theoretical and/or physical chemistry</classCode><classCode scheme="halTypology" n="COUV">Book section</classCode></textClass><abstract xml:lang="en">Protein-protein interactions and the formation of protein-protein complexes are central to many biological processes. Protein docking is the task of calculating the three-dimensional structure of a protein complex starting from the individual structures of the constituent proteins. Although proteins are intrinsically flexible, most docking algorithms begin by assuming that the proteins to be docked are rigid. This assumption allows fast rigid-body docking techniques to be used to generate a relatively small list of candidate docking poses which may subsequently be refined using more computationally intensive force-field based approaches. Protein docking predictions are helping to provide a better physical picture of protein-protein interactions, and the use of protein docking is becoming an increasingly important way to help identify potential drug targets. This chapter gives an overview of current theory and practice in the use of computational and data-based protein docking techniques, with particular focus on using fast Fourier transform techniques and modern graphics processors to accelerate the rigid body part of a docking calculation.</abstract></profileDesc></hal></record>Pour manipuler ce document sous Unix (Dilib)
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