Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry
Identifieur interne : 004754 ( Hal/Corpus ); précédent : 004753; suivant : 004755Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry
Auteurs : David W. Ritchie ; Sergei GrudininSource :
- Journal of Applied Crystallography [ 0021-8898 ] ; 2016-02-01.
English descriptors
Abstract
A novel fast Fourier transform-based ab inito docking algorithm called SAM is presented, for building perfectly symmetrical models of protein complexes with arbitrary point group symmetry. The basic approach uses a novel and very fast one-dimensional symmetry-constrained spherical polar Fourier search to assemble cyclic Cn systems from a given protein monomer. Structures with higher-order (Dn, T, O and I) point group symmetries may be built using a subsequent symmetry-constrained Fourier domain search to assemble trimeric sub-units. The results reported here show that the SAM algorithm can correctly assemble monomers of up to around 500 residues to produce a near-native complex structure with the given point group symmetry in 17 out of 18 test cases. The SAM program may be downloaded for academic use at http://sam.loria.fr/.
Url:
DOI: 10.1107/S1600576715022931
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Hal:hal-01261402Le document en format XML
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<front><div type="abstract" xml:lang="en">A novel fast Fourier transform-based ab inito docking algorithm called SAM is presented, for building perfectly symmetrical models of protein complexes with arbitrary point group symmetry. The basic approach uses a novel and very fast one-dimensional symmetry-constrained spherical polar Fourier search to assemble cyclic Cn systems from a given protein monomer. Structures with higher-order (Dn, T, O and I) point group symmetries may be built using a subsequent symmetry-constrained Fourier domain search to assemble trimeric sub-units. The results reported here show that the SAM algorithm can correctly assemble monomers of up to around 500 residues to produce a near-native complex structure with the given point group symmetry in 17 out of 18 test cases. The SAM program may be downloaded for academic use at http://sam.loria.fr/.</div>
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<idno type="halRefHtml">Journal of Applied Crystallography, International Union of Crystallography, 2016, 49 (1), pp.158-167. <10.1107/S1600576715022931></idno>
<idno type="halRef">Journal of Applied Crystallography, International Union of Crystallography, 2016, 49 (1), pp.158-167. <10.1107/S1600576715022931></idno>
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<seriesStmt><idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
<idno type="stamp" n="UNIV-PMF_GRENOBLE" p="UGA">Université Pierre-Mendès-France - Grenoble II</idno>
<idno type="stamp" n="INPG" p="UGA">Institut polytechnique de Grenoble</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="INRIA-NANCY-GRAND-EST">INRIA Nancy - Grand Est</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="LJK" p="UGA">Laboratoire Jean Kuntzmann</idno>
<idno type="stamp" n="INRIA_TEST">INRIA - Institut National de Recherche en Informatique et en Automatique</idno>
<idno type="stamp" n="UNIV-LORRAINE">Université de Lorraine</idno>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry</title>
<author role="aut"><persName><forename type="first">David W.</forename>
<surname>Ritchie</surname>
</persName>
<email>Dave.Ritchie@loria.fr</email>
<idno type="idHal">david-ritchie</idno>
<idno type="halAuthorId">1187734</idno>
<affiliation ref="#struct-420402"></affiliation>
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<author role="aut"><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">1091545</idno>
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</author>
</analytic>
<monogr><idno type="halJournalId" status="VALID">15074</idno>
<idno type="issn">0021-8898</idno>
<idno type="eissn">1600-5767</idno>
<title level="j">Journal of Applied Crystallography</title>
<imprint><publisher>International Union of Crystallography</publisher>
<biblScope unit="volume">49</biblScope>
<biblScope unit="issue">1</biblScope>
<biblScope unit="pp">158-167</biblScope>
<date type="datePub">2016-02-01</date>
<date type="dateEpub">2015-11-30</date>
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<idno type="doi">10.1107/S1600576715022931</idno>
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<profileDesc><langUsage><language ident="en">English</language>
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<textClass><keywords scheme="author"><term xml:lang="en"> symmetry docking</term>
<term xml:lang="en"> point group symmetry</term>
<term xml:lang="en">protein docking</term>
<term xml:lang="en"> polar Fourier correlation</term>
</keywords>
<classCode scheme="halDomain" n="info.info-mo">Computer Science [cs]/Modeling and Simulation</classCode>
<classCode scheme="halDomain" n="info.info-bi">Computer Science [cs]/Bioinformatics [q-bio.QM]</classCode>
<classCode scheme="halDomain" n="sdv.bbm.bs">Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]</classCode>
<classCode scheme="halTypology" n="ART">Journal articles</classCode>
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<abstract xml:lang="en">A novel fast Fourier transform-based ab inito docking algorithm called SAM is presented, for building perfectly symmetrical models of protein complexes with arbitrary point group symmetry. The basic approach uses a novel and very fast one-dimensional symmetry-constrained spherical polar Fourier search to assemble cyclic Cn systems from a given protein monomer. Structures with higher-order (Dn, T, O and I) point group symmetries may be built using a subsequent symmetry-constrained Fourier domain search to assemble trimeric sub-units. The results reported here show that the SAM algorithm can correctly assemble monomers of up to around 500 residues to produce a near-native complex structure with the given point group symmetry in 17 out of 18 test cases. The SAM program may be downloaded for academic use at http://sam.loria.fr/.</abstract>
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