DockTrina: Docking triangular protein trimers
Identifieur interne : 006D09 ( Hal/Corpus ); précédent : 006D08; suivant : 006D10DockTrina: Docking triangular protein trimers
Auteurs : Petr Popov ; David Ritchie ; Sergei GrudininSource :
English descriptors
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Abstract
In spite of the abundance of oligomeric proteins within a cell, the structural characterization of protein-protein interactions is still a challenging task. In particular, many of these interactions involve heteromeric complexes, which are relatively difficult to determine experimentally. Hence there is growing interest in using computational techniques to model such complexes. However, assembling large heteromeric complexes computationally is a highly combinatorial problem. Nonetheless the problem can be simplified greatly by considering interactions between protein trimers. After dimers and monomers, triangular trimers (i.e. trimers with pair-wise contacts between all three pairs of proteins) are the most frequently observed quaternary structural motifs according to the three-dimensional (3D) complex database. This article presents DockTrina, a novel protein docking method for modeling the 3D structures of nonsymmetrical triangular trimers. The method takes as input pair-wise contact predictions from a rigid body docking program. It then scans and scores all possible combinations of pairs of monomers using a very fast root mean square deviation test. Finally, it ranks the predictions using a scoring function which combines triples of pair-wise contact terms and a geometric clash penalty term. The overall approach takes less than 2 min per complex on a modern desktop computer. The method is tested and validated using a benchmark set of 220 bound and seven unbound protein trimer structures.
Url:
DOI: 10.1002/prot.24344
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Hal:hal-00880359Le document en format XML
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In particular, many of these interactions involve heteromeric complexes, which are relatively difficult to determine experimentally. Hence there is growing interest in using computational techniques to model such complexes. However, assembling large heteromeric complexes computationally is a highly combinatorial problem. Nonetheless the problem can be simplified greatly by considering interactions between protein trimers. After dimers and monomers, triangular trimers (i.e. trimers with pair-wise contacts between all three pairs of proteins) are the most frequently observed quaternary structural motifs according to the three-dimensional (3D) complex database. This article presents DockTrina, a novel protein docking method for modeling the 3D structures of nonsymmetrical triangular trimers. The method takes as input pair-wise contact predictions from a rigid body docking program. It then scans and scores all possible combinations of pairs of monomers using a very fast root mean square deviation test. Finally, it ranks the predictions using a scoring function which combines triples of pair-wise contact terms and a geometric clash penalty term. The overall approach takes less than 2 min per complex on a modern desktop computer. The method is tested and validated using a benchmark set of 220 bound and seven unbound protein trimer structures.</div></front></TEI><hal api="V3"><titleStmt><title xml:lang="sv">DockTrina: Docking triangular protein trimers</title><author role="aut"><persName><forename type="first">Petr</forename><surname>Popov</surname></persName><email></email><idno type="halauthor">909043</idno><orgName ref="#struct-300009"></orgName><affiliation ref="#struct-55137"></affiliation></author><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><author role="crp"><persName><forename type="first">Sergei</forename><surname>Grudinin</surname></persName><email>sergei.grudinin@inria.fr</email><ptr type="url" target="http://nano-d.inrialpes.fr/sergei-grudinin/"></ptr><idno type="halauthor">781212</idno><orgName ref="#struct-441569"></orgName><affiliation ref="#struct-55137"></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">2013-11-05 21:07:43</date><date type="whenModified">2015-09-22 01:12:03</date><date type="whenReleased">2013-11-05 21:07:43</date><date type="whenProduced">2014-01</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-00880359</idno><idno type="halUri">https://hal.inria.fr/hal-00880359</idno><idno type="halBibtex">popov:hal-00880359</idno><idno type="halRefHtml">Proteins: Structure, Function, and Genetics, Wiley, 2014, 82 (1), pp.34-44. <10.1002/prot.24344></idno><idno type="halRef">Proteins: Structure, Function, and Genetics, Wiley, 2014, 82 (1), pp.34-44. <10.1002/prot.24344></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="UNIV-GRENOBLE1" p="UGA">Université Joseph Fourier - Grenoble I</idno><idno type="stamp" n="INRIA-RHA">INRIA Grenoble - Rhône-Alpes</idno><idno type="stamp" n="INRIA-LORRAINE">INRIA Nancy - Grand Est</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-TALC" p="LORIA">Traitement automatique des langues et des connaissances</idno><idno type="stamp" n="LORIA">LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications</idno><idno type="stamp" n="INPG" p="UGA">Institut polytechnique de Grenoble</idno><idno type="stamp" n="LJK_MAD" p="LJK">Département Modèles et Algorithmes Déterministes</idno><idno type="stamp" n="LJK_MAD_NANO-D" p="LJK_MAD">NANO-D</idno><idno type="stamp" n="LJK" p="UGA">Laboratoire Jean Kuntzmann</idno><idno type="stamp" n="UGA">HAL Grenoble Alpes</idno><idno type="stamp" n="UNIV-PMF_GRENOBLE" p="UGA">Université Pierre-Mendès-France - Grenoble II</idno><idno type="stamp" n="CENTRALESUPELEC">Ecole CentraleSupélec</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><note type="peer" n="1">Yes</note></notesStmt><sourceDesc><biblStruct><analytic><title xml:lang="sv">DockTrina: Docking triangular protein trimers</title><author role="aut"><persName><forename type="first">Petr</forename><surname>Popov</surname></persName><idno type="halAuthorId">909043</idno><orgName ref="#struct-300009"></orgName><affiliation ref="#struct-55137"></affiliation></author><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><author role="crp"><persName><forename type="first">Sergei</forename><surname>Grudinin</surname></persName><email>sergei.grudinin@inria.fr</email><ptr type="url" target="http://nano-d.inrialpes.fr/sergei-grudinin/"></ptr><idno type="halAuthorId">781212</idno><orgName ref="#struct-441569"></orgName><affiliation ref="#struct-55137"></affiliation></author></analytic><monogr><idno type="halJournalId" status="VALID">20582</idno><title level="j">Proteins: Structure, Function, and Genetics</title><imprint><publisher>Wiley</publisher><biblScope unit="volume">82</biblScope><biblScope unit="issue">1</biblScope><biblScope unit="pp">34-44</biblScope><date type="datePub">2014-01</date></imprint></monogr><idno type="doi">10.1002/prot.24344</idno><ref type="seeAlso">https://team.inria.fr/nano-d/software/docktrina/</ref></biblStruct></sourceDesc><profileDesc><langUsage><language ident="en">English</language></langUsage><textClass><keywords scheme="author"><term xml:lang="en">protein domains</term><term xml:lang="en">protein structure prediction</term><term xml:lang="en">protein-protein interactions</term><term xml:lang="en">computational docking</term><term xml:lang="en">algorithms</term><term xml:lang="en">combinatorial search</term><term xml:lang="en">software development</term></keywords><classCode scheme="halDomain" n="info.info-bi">Computer Science [cs]/Bioinformatics [q-bio.QM]</classCode><classCode scheme="halDomain" n="sdv.bibs">Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]</classCode><classCode scheme="halTypology" n="ART">Journal articles</classCode></textClass><abstract xml:lang="en">In spite of the abundance of oligomeric proteins within a cell, the structural characterization of protein-protein interactions is still a challenging task. In particular, many of these interactions involve heteromeric complexes, which are relatively difficult to determine experimentally. Hence there is growing interest in using computational techniques to model such complexes. However, assembling large heteromeric complexes computationally is a highly combinatorial problem. Nonetheless the problem can be simplified greatly by considering interactions between protein trimers. After dimers and monomers, triangular trimers (i.e. trimers with pair-wise contacts between all three pairs of proteins) are the most frequently observed quaternary structural motifs according to the three-dimensional (3D) complex database. This article presents DockTrina, a novel protein docking method for modeling the 3D structures of nonsymmetrical triangular trimers. The method takes as input pair-wise contact predictions from a rigid body docking program. It then scans and scores all possible combinations of pairs of monomers using a very fast root mean square deviation test. Finally, it ranks the predictions using a scoring function which combines triples of pair-wise contact terms and a geometric clash penalty term. The overall approach takes less than 2 min per complex on a modern desktop computer. The method is tested and validated using a benchmark set of 220 bound and seven unbound protein trimer structures.</abstract></profileDesc></hal></record>Pour manipuler ce document sous Unix (Dilib)
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