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
Links to Exploration step
Hal:hal-01261402Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry</title><author><name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W." last="Ritchie">David W. Ritchie</name><affiliation><hal:affiliation type="researchteam" xml:id="struct-420402" status="VALID"><idno type="RNSR">201521171B</idno><orgName>Computational Algorithms for Protein Structures and Interactions</orgName><orgName type="acronym">CAPSID</orgName><desc><address><country key="FR"></country></address><ref type="url">http://www.inria.fr/equipes/capsid</ref></desc><listRelation><relation active="#struct-129671" type="direct"></relation><relation active="#struct-300009" type="indirect"></relation><relation active="#struct-423090" type="direct"></relation><relation active="#struct-206040" type="indirect"></relation><relation active="#struct-413289" type="indirect"></relation><relation name="UMR7503" active="#struct-441569" type="indirect"></relation></listRelation><tutelles><tutelle active="#struct-129671" type="direct"><org type="laboratory" xml:id="struct-129671" status="VALID"><idno type="RNSR">198618246Y</idno><orgName>INRIA Nancy - Grand Est</orgName><desc><address><addrLine>615 rue du Jardin Botanique 54600 Villers-lès-Nancy</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/nancy</ref></desc><listRelation><relation active="#struct-300009" type="direct"></relation></listRelation></org></tutelle><tutelle active="#struct-300009" type="indirect"><org type="institution" xml:id="struct-300009" status="VALID"><orgName>Institut National de Recherche en Informatique et en Automatique</orgName><orgName type="acronym">Inria</orgName><desc><address><addrLine>Domaine de VoluceauRocquencourt - BP 10578153 Le Chesnay Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/en/</ref></desc></org></tutelle><tutelle active="#struct-423090" type="direct"><org type="department" xml:id="struct-423090" status="VALID"><orgName>Department of Complex Systems, Artificial Intelligence & Robotics</orgName><orgName type="acronym">LORIA - AIS</orgName><desc><address><country key="FR"></country></address><ref type="url">http://www.loria.fr/la-recherche-en/departements/complex-system-and-artificial-intelligence</ref></desc><listRelation><relation active="#struct-206040" type="direct"></relation><relation active="#struct-300009" type="indirect"></relation><relation active="#struct-413289" type="indirect"></relation><relation name="UMR7503" active="#struct-441569" type="indirect"></relation></listRelation></org></tutelle><tutelle active="#struct-206040" type="indirect"><org type="laboratory" xml:id="struct-206040" status="VALID"><idno type="IdRef">067077927</idno><idno type="RNSR">198912571S</idno><idno type="IdUnivLorraine">[UL]RSI--</idno><orgName>Laboratoire Lorrain de Recherche en Informatique et ses Applications</orgName><orgName type="acronym">LORIA</orgName><date type="start">2012-01-01</date><desc><address><addrLine>Campus Scientifique BP 239 54506 Vandoeuvre-lès-Nancy Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.loria.fr</ref></desc><listRelation><relation active="#struct-300009" type="direct"></relation><relation active="#struct-413289" type="direct"></relation><relation name="UMR7503" active="#struct-441569" type="direct"></relation></listRelation></org></tutelle><tutelle active="#struct-413289" type="indirect"><org type="institution" xml:id="struct-413289" status="VALID"><idno type="IdRef">157040569</idno><idno type="IdUnivLorraine">[UL]100--</idno><orgName>Université de Lorraine</orgName><orgName type="acronym">UL</orgName><date type="start">2012-01-01</date><desc><address><addrLine>34 cours Léopold - CS 25233 - 54052 Nancy cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.univ-lorraine.fr/</ref></desc></org></tutelle><tutelle name="UMR7503" active="#struct-441569" type="indirect"><org type="institution" xml:id="struct-441569" status="VALID"><idno type="ISNI">0000000122597504</idno><idno type="IdRef">02636817X</idno><orgName>Centre National de la Recherche Scientifique</orgName><orgName type="acronym">CNRS</orgName><date type="start">1939-10-19</date><desc><address><country key="FR"></country></address><ref type="url">http://www.cnrs.fr/</ref></desc></org></tutelle></tutelles></hal:affiliation></affiliation></author><author><name sortKey="Grudinin, Sergei" sort="Grudinin, Sergei" uniqKey="Grudinin S" first="Sergei" last="Grudinin">Sergei Grudinin</name><affiliation><hal:affiliation type="researchteam" xml:id="struct-55137" status="VALID"><idno type="RNSR">200820953V</idno><orgName>Algorithms for Modeling and Simulation of Nanosystems</orgName><orgName type="acronym">NANO-D</orgName><desc><address><addrLine>Inria GIANT DRT/LETI/DACLE Batiment 51C - Minatec Campus 17 rue des Martyrs 38054 Grenoble Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/equipes/nano-d</ref></desc><listRelation><relation active="#struct-2497" type="direct"></relation><relation active="#struct-300009" type="indirect"></relation><relation active="#struct-24474" type="direct"></relation><relation active="#struct-3886" type="indirect"></relation><relation active="#struct-51016" type="indirect"></relation><relation active="#struct-300339" type="indirect"></relation><relation name="UMR5224" active="#struct-441569" type="indirect"></relation><relation active="#struct-300275" type="direct"></relation></listRelation><tutelles><tutelle active="#struct-2497" type="direct"><org type="laboratory" xml:id="struct-2497" status="VALID"><idno type="RNSR">199218244V</idno><orgName>Inria Grenoble - Rhône-Alpes</orgName><desc><address><addrLine>Inovallée655 avenue de l'Europe38330 Montbonnot</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/centre/grenoble</ref></desc><listRelation><relation active="#struct-300009" type="direct"></relation></listRelation></org></tutelle><tutelle active="#struct-300009" type="indirect"><org type="institution" xml:id="struct-300009" status="VALID"><orgName>Institut National de Recherche en Informatique et en Automatique</orgName><orgName type="acronym">Inria</orgName><desc><address><addrLine>Domaine de VoluceauRocquencourt - BP 10578153 Le Chesnay Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/en/</ref></desc></org></tutelle><tutelle active="#struct-24474" type="direct"><org type="laboratory" xml:id="struct-24474" status="VALID"><orgName>Laboratoire Jean Kuntzmann</orgName><orgName type="acronym">LJK</orgName><desc><address><addrLine>Tour IRMA 51 rue des Mathématiques - 53 38041 GRENOBLE CEDEX 9</addrLine><country key="FR"></country></address><ref type="url">http://ljk.imag.fr</ref></desc><listRelation><relation active="#struct-3886" type="direct"></relation><relation active="#struct-51016" type="direct"></relation><relation active="#struct-300339" type="direct"></relation><relation name="UMR5224" active="#struct-441569" type="direct"></relation></listRelation></org></tutelle><tutelle active="#struct-3886" type="indirect"><org type="institution" xml:id="struct-3886" status="OLD"><orgName>Université Pierre Mendès France</orgName><orgName type="acronym">Grenoble 2 UPMF</orgName><date type="end">2015-12-31</date><desc><address><addrLine>BP 47 - 38040 Grenoble Cedex 9</addrLine><country key="FR"></country></address><ref type="url">http://www.upmf-grenoble.fr/</ref></desc></org></tutelle><tutelle active="#struct-51016" type="indirect"><org type="institution" xml:id="struct-51016" status="OLD"><orgName>Université Joseph Fourier</orgName><orgName type="acronym">UJF</orgName><date type="end">2015-12-31</date><desc><address><addrLine>BP 53 - 38041 Grenoble Cedex 9</addrLine><country key="FR"></country></address><ref type="url">http://www.ujf-grenoble.fr/</ref></desc></org></tutelle><tutelle active="#struct-300339" type="indirect"><org type="institution" xml:id="struct-300339" status="VALID"><orgName>Institut Polytechnique de Grenoble - Grenoble Institute of Technology</orgName><desc><address><country key="FR"></country></address></desc></org></tutelle><tutelle name="UMR5224" active="#struct-441569" type="indirect"><org type="institution" xml:id="struct-441569" status="VALID"><idno type="ISNI">0000000122597504</idno><idno type="IdRef">02636817X</idno><orgName>Centre National de la Recherche Scientifique</orgName><orgName type="acronym">CNRS</orgName><date type="start">1939-10-19</date><desc><address><country key="FR"></country></address><ref type="url">http://www.cnrs.fr/</ref></desc></org></tutelle><tutelle active="#struct-300275" type="direct"><org type="institution" xml:id="struct-300275" status="VALID"><orgName>Institut National Polytechnique de Grenoble (INPG)</orgName><desc><address><country key="FR"></country></address></desc></org></tutelle></tutelles></hal:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">HAL</idno><idno type="RBID">Hal:hal-01261402</idno><idno type="halId">hal-01261402</idno><idno type="halUri">https://hal.inria.fr/hal-01261402</idno><idno type="url">https://hal.inria.fr/hal-01261402</idno><idno type="doi">10.1107/S1600576715022931</idno><date when="2016-02-01">2016-02-01</date><idno type="wicri:Area/Hal/Corpus">004754</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry</title><author><name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W." last="Ritchie">David W. Ritchie</name><affiliation><hal:affiliation type="researchteam" xml:id="struct-420402" status="VALID"><idno type="RNSR">201521171B</idno><orgName>Computational Algorithms for Protein Structures and Interactions</orgName><orgName type="acronym">CAPSID</orgName><desc><address><country key="FR"></country></address><ref type="url">http://www.inria.fr/equipes/capsid</ref></desc><listRelation><relation active="#struct-129671" type="direct"></relation><relation active="#struct-300009" type="indirect"></relation><relation active="#struct-423090" type="direct"></relation><relation active="#struct-206040" type="indirect"></relation><relation active="#struct-413289" type="indirect"></relation><relation name="UMR7503" active="#struct-441569" type="indirect"></relation></listRelation><tutelles><tutelle active="#struct-129671" type="direct"><org type="laboratory" xml:id="struct-129671" status="VALID"><idno type="RNSR">198618246Y</idno><orgName>INRIA Nancy - Grand Est</orgName><desc><address><addrLine>615 rue du Jardin Botanique 54600 Villers-lès-Nancy</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/nancy</ref></desc><listRelation><relation active="#struct-300009" type="direct"></relation></listRelation></org></tutelle><tutelle active="#struct-300009" type="indirect"><org type="institution" xml:id="struct-300009" status="VALID"><orgName>Institut National de Recherche en Informatique et en Automatique</orgName><orgName type="acronym">Inria</orgName><desc><address><addrLine>Domaine de VoluceauRocquencourt - BP 10578153 Le Chesnay Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/en/</ref></desc></org></tutelle><tutelle active="#struct-423090" type="direct"><org type="department" xml:id="struct-423090" status="VALID"><orgName>Department of Complex Systems, Artificial Intelligence & Robotics</orgName><orgName type="acronym">LORIA - AIS</orgName><desc><address><country key="FR"></country></address><ref type="url">http://www.loria.fr/la-recherche-en/departements/complex-system-and-artificial-intelligence</ref></desc><listRelation><relation active="#struct-206040" type="direct"></relation><relation active="#struct-300009" type="indirect"></relation><relation active="#struct-413289" type="indirect"></relation><relation name="UMR7503" active="#struct-441569" type="indirect"></relation></listRelation></org></tutelle><tutelle active="#struct-206040" type="indirect"><org type="laboratory" xml:id="struct-206040" status="VALID"><idno type="IdRef">067077927</idno><idno type="RNSR">198912571S</idno><idno type="IdUnivLorraine">[UL]RSI--</idno><orgName>Laboratoire Lorrain de Recherche en Informatique et ses Applications</orgName><orgName type="acronym">LORIA</orgName><date type="start">2012-01-01</date><desc><address><addrLine>Campus Scientifique BP 239 54506 Vandoeuvre-lès-Nancy Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.loria.fr</ref></desc><listRelation><relation active="#struct-300009" type="direct"></relation><relation active="#struct-413289" type="direct"></relation><relation name="UMR7503" active="#struct-441569" type="direct"></relation></listRelation></org></tutelle><tutelle active="#struct-413289" type="indirect"><org type="institution" xml:id="struct-413289" status="VALID"><idno type="IdRef">157040569</idno><idno type="IdUnivLorraine">[UL]100--</idno><orgName>Université de Lorraine</orgName><orgName type="acronym">UL</orgName><date type="start">2012-01-01</date><desc><address><addrLine>34 cours Léopold - CS 25233 - 54052 Nancy cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.univ-lorraine.fr/</ref></desc></org></tutelle><tutelle name="UMR7503" active="#struct-441569" type="indirect"><org type="institution" xml:id="struct-441569" status="VALID"><idno type="ISNI">0000000122597504</idno><idno type="IdRef">02636817X</idno><orgName>Centre National de la Recherche Scientifique</orgName><orgName type="acronym">CNRS</orgName><date type="start">1939-10-19</date><desc><address><country key="FR"></country></address><ref type="url">http://www.cnrs.fr/</ref></desc></org></tutelle></tutelles></hal:affiliation></affiliation></author><author><name sortKey="Grudinin, Sergei" sort="Grudinin, Sergei" uniqKey="Grudinin S" first="Sergei" last="Grudinin">Sergei Grudinin</name><affiliation><hal:affiliation type="researchteam" xml:id="struct-55137" status="VALID"><idno type="RNSR">200820953V</idno><orgName>Algorithms for Modeling and Simulation of Nanosystems</orgName><orgName type="acronym">NANO-D</orgName><desc><address><addrLine>Inria GIANT DRT/LETI/DACLE Batiment 51C - Minatec Campus 17 rue des Martyrs 38054 Grenoble Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/equipes/nano-d</ref></desc><listRelation><relation active="#struct-2497" type="direct"></relation><relation active="#struct-300009" type="indirect"></relation><relation active="#struct-24474" type="direct"></relation><relation active="#struct-3886" type="indirect"></relation><relation active="#struct-51016" type="indirect"></relation><relation active="#struct-300339" type="indirect"></relation><relation name="UMR5224" active="#struct-441569" type="indirect"></relation><relation active="#struct-300275" type="direct"></relation></listRelation><tutelles><tutelle active="#struct-2497" type="direct"><org type="laboratory" xml:id="struct-2497" status="VALID"><idno type="RNSR">199218244V</idno><orgName>Inria Grenoble - Rhône-Alpes</orgName><desc><address><addrLine>Inovallée655 avenue de l'Europe38330 Montbonnot</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/centre/grenoble</ref></desc><listRelation><relation active="#struct-300009" type="direct"></relation></listRelation></org></tutelle><tutelle active="#struct-300009" type="indirect"><org type="institution" xml:id="struct-300009" status="VALID"><orgName>Institut National de Recherche en Informatique et en Automatique</orgName><orgName type="acronym">Inria</orgName><desc><address><addrLine>Domaine de VoluceauRocquencourt - BP 10578153 Le Chesnay Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/en/</ref></desc></org></tutelle><tutelle active="#struct-24474" type="direct"><org type="laboratory" xml:id="struct-24474" status="VALID"><orgName>Laboratoire Jean Kuntzmann</orgName><orgName type="acronym">LJK</orgName><desc><address><addrLine>Tour IRMA 51 rue des Mathématiques - 53 38041 GRENOBLE CEDEX 9</addrLine><country key="FR"></country></address><ref type="url">http://ljk.imag.fr</ref></desc><listRelation><relation active="#struct-3886" type="direct"></relation><relation active="#struct-51016" type="direct"></relation><relation active="#struct-300339" type="direct"></relation><relation name="UMR5224" active="#struct-441569" type="direct"></relation></listRelation></org></tutelle><tutelle active="#struct-3886" type="indirect"><org type="institution" xml:id="struct-3886" status="OLD"><orgName>Université Pierre Mendès France</orgName><orgName type="acronym">Grenoble 2 UPMF</orgName><date type="end">2015-12-31</date><desc><address><addrLine>BP 47 - 38040 Grenoble Cedex 9</addrLine><country key="FR"></country></address><ref type="url">http://www.upmf-grenoble.fr/</ref></desc></org></tutelle><tutelle active="#struct-51016" type="indirect"><org type="institution" xml:id="struct-51016" status="OLD"><orgName>Université Joseph Fourier</orgName><orgName type="acronym">UJF</orgName><date type="end">2015-12-31</date><desc><address><addrLine>BP 53 - 38041 Grenoble Cedex 9</addrLine><country key="FR"></country></address><ref type="url">http://www.ujf-grenoble.fr/</ref></desc></org></tutelle><tutelle active="#struct-300339" type="indirect"><org type="institution" xml:id="struct-300339" status="VALID"><orgName>Institut Polytechnique de Grenoble - Grenoble Institute of Technology</orgName><desc><address><country key="FR"></country></address></desc></org></tutelle><tutelle name="UMR5224" active="#struct-441569" type="indirect"><org type="institution" xml:id="struct-441569" status="VALID"><idno type="ISNI">0000000122597504</idno><idno type="IdRef">02636817X</idno><orgName>Centre National de la Recherche Scientifique</orgName><orgName type="acronym">CNRS</orgName><date type="start">1939-10-19</date><desc><address><country key="FR"></country></address><ref type="url">http://www.cnrs.fr/</ref></desc></org></tutelle><tutelle active="#struct-300275" type="direct"><org type="institution" xml:id="struct-300275" status="VALID"><orgName>Institut National Polytechnique de Grenoble (INPG)</orgName><desc><address><country key="FR"></country></address></desc></org></tutelle></tutelles></hal:affiliation></affiliation></author></analytic><idno type="DOI">10.1107/S1600576715022931</idno><series><title level="j">Journal of Applied Crystallography</title><idno type="ISSN">0021-8898</idno><imprint><date type="datePub">2016-02-01</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="mix" xml:lang="en"><term> point group symmetry</term><term> polar Fourier correlation</term><term> symmetry docking</term><term>protein docking</term></keywords></textClass></profileDesc></teiHeader><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></front></TEI><hal api="V3"><titleStmt><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="halauthor">1187734</idno><affiliation ref="#struct-420402"></affiliation></author><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="halauthor">1091545</idno><affiliation ref="#struct-55137"></affiliation></author><editor role="depositor"><persName><forename>Nano-D</forename><surname>Equipe</surname></persName><email>francois.rousse@inria.fr</email></editor><funder ref="#projanr-34711"></funder></titleStmt><editionStmt><edition n="v1" type="current"><date type="whenSubmitted">2016-02-01 14:21:55</date><date type="whenModified">2016-02-07 23:24:11</date><date type="whenReleased">2016-02-02 10:22:33</date><date type="whenProduced">2016-02-01</date><date type="whenEndEmbargoed">2016-02-01</date><ref type="file" target="https://hal.inria.fr/hal-01261402/document"><date notBefore="2016-02-01"></date></ref><ref type="file" subtype="greenPublisher" n="1" target="https://hal.inria.fr/hal-01261402/file/ritchie_grudinin_jac_2016.pdf"><date notBefore="2016-02-01"></date></ref></edition><respStmt><resp>contributor</resp><name key="188371"><persName><forename>Nano-D</forename><surname>Equipe</surname></persName><email>francois.rousse@inria.fr</email></name></respStmt></editionStmt><publicationStmt><distributor>CCSD</distributor><idno type="halId">hal-01261402</idno><idno type="halUri">https://hal.inria.fr/hal-01261402</idno><idno type="halBibtex">ritchie:hal-01261402</idno><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></publicationStmt><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><idno type="stamp" n="INRIA2">INRIA 2</idno><idno type="stamp" n="LORIA2">Publications du LORIA</idno><idno type="stamp" n="UGA">HAL Grenoble Alpes</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></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="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></author><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><affiliation ref="#struct-55137"></affiliation></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></imprint></monogr><idno type="doi">10.1107/S1600576715022931</idno></biblStruct></sourceDesc><profileDesc><langUsage><language ident="en">English</language></langUsage><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></textClass><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></profileDesc></hal></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Lorraine/explor/InforLorV4/Data/Hal/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 004754 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Hal/Corpus/biblio.hfd -nk 004754 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Lorraine
|area= InforLorV4
|flux= Hal
|étape= Corpus
|type= RBID
|clé= Hal:hal-01261402
|texte= Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry
}}
| This area was generated with Dilib version V0.6.33. |  |