InforLorV4, Pmc, Checkpoint, bibRecord, 000070

HexServer: an FFT-based protein docking server powered by graphics processors

Identifieur interne : 000070 ( Pmc/Checkpoint ); précédent : 000069; suivant : 000071

HexServer: an FFT-based protein docking server powered by graphics processors

Auteurs : Gary Macindoe [Royaume-Uni] ; Lazaros Mavridis ; Vishwesh Venkatraman ; Marie-Dominique Devignes [France] ; David W. Ritchie

Source :

Nucleic Acids Research [ 0305-1048 ] ; 2010.

RBID : PMC:2896144

Abstract

HexServer (http://hexserver.loria.fr/) is the first Fourier transform (FFT)-based protein docking server to be powered by graphics processors. Using two graphics processors simultaneously, a typical 6D docking run takes ∼15 s, which is up to two orders of magnitude faster than conventional FFT-based docking approaches using comparable resolution and scoring functions. The server requires two protein structures in PDB format to be uploaded, and it produces a ranked list of up to 1000 docking predictions. Knowledge of one or both protein binding sites may be used to focus and shorten the calculation when such information is available. The first 20 predictions may be accessed individually, and a single file of all predicted orientations may be downloaded as a compressed multi-model PDB file. The server is publicly available and does not require any registration or identification by the user.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896144

DOI: 10.1093/nar/gkq311
PubMed: 20444869
PubMed Central: 2896144

Affiliations:

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Le document en format XML

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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
  <front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id>
<journal-id journal-id-type="iso-abbrev">Nucleic Acids Res</journal-id>
<journal-id journal-id-type="publisher-id">nar</journal-id>
<journal-id journal-id-type="hwp">nar</journal-id>
<journal-title-group><journal-title>Nucleic Acids Research</journal-title>
</journal-title-group>
<issn pub-type="ppub">0305-1048</issn>
<issn pub-type="epub">1362-4962</issn>
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<article-meta><article-id pub-id-type="pmid">20444869</article-id>
<article-id pub-id-type="pmc">2896144</article-id>
<article-id pub-id-type="doi">10.1093/nar/gkq311</article-id>
<article-id pub-id-type="publisher-id">gkq311</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Articles</subject>
</subj-group>
</article-categories>
<title-group><article-title>HexServer: an FFT-based protein docking server powered by graphics processors</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Macindoe</surname>
<given-names>Gary</given-names>
</name>
<xref ref-type="aff" rid="AFF1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mavridis</surname>
<given-names>Lazaros</given-names>
</name>
<xref ref-type="aff" rid="AFF1"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Venkatraman</surname>
<given-names>Vishwesh</given-names>
</name>
<xref ref-type="aff" rid="AFF1"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Devignes</surname>
<given-names>Marie-Dominique</given-names>
</name>
<xref ref-type="aff" rid="AFF1"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ritchie</surname>
<given-names>David W.</given-names>
</name>
<xref ref-type="aff" rid="AFF1"><sup>2</sup>
</xref>
<xref ref-type="corresp" rid="COR1">*</xref>
</contrib>
</contrib-group>
<aff id="AFF1"><sup>1</sup>
Department of Computing Science, Lillybank Gardens, University of Glasgow, G12 8QQ Scotland, UK,<sup>2</sup>
Orpailleur Team (INRIA) and<sup>3</sup>
Orpailleur Team (CNRS), LORIA, 615 Jardin du Botanique, 54506 Vandoeuvre-lès-Nancy, France</aff>
<author-notes><corresp id="COR1">*To whom correspondence should be addressed. Tel: <phone>+33 3 83 59 30 45</phone>
; Fax: <fax>+33 3 83 59 30 79</fax>
; Email: <email>dave.ritchie@loria.fr</email>
</corresp>
</author-notes>
<pub-date pub-type="ppub"><day>1</day>
<month>7</month>
<year>2010</year>
</pub-date>
<pub-date pub-type="epub"><day>5</day>
<month>5</month>
<year>2010</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>5</day>
<month>5</month>
<year>2010</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the 
 							. </pmc-comment>
      <volume>38</volume>
<issue>Web Server issue</issue>
<fpage>W445</fpage>
<lpage>W449</lpage>
<history><date date-type="received"><day>28</day>
<month>1</month>
<year>2010</year>
</date>
<date date-type="rev-recd"><day>25</day>
<month>3</month>
<year>2010</year>
</date>
<date date-type="accepted"><day>17</day>
<month>4</month>
<year>2010</year>
</date>
</history>
<permissions><copyright-statement>© The Author(s) 2010. Published by Oxford University Press.</copyright-statement>
<copyright-year>2010</copyright-year>
<license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.5"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.5">http://creativecommons.org/licenses/by-nc/2.5</ext-link>
), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<abstract><p>HexServer (<ext-link ext-link-type="uri" xlink:href="http://hexserver.loria.fr/">http://hexserver.loria.fr/</ext-link>
) is the first Fourier transform (FFT)-based protein docking server to be powered by graphics processors. Using two graphics processors simultaneously, a typical 6D docking run takes ∼15 s, which is up to two orders of magnitude faster than conventional FFT-based docking approaches using comparable resolution and scoring functions. The server requires two protein structures in PDB format to be uploaded, and it produces a ranked list of up to 1000 docking predictions. Knowledge of one or both protein binding sites may be used to focus and shorten the calculation when such information is available. The first 20 predictions may be accessed individually, and a single file of all predicted orientations may be downloaded as a compressed multi-model PDB file. The server is publicly available and does not require any registration or identification by the user.</p>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>France</li>
<li>Royaume-Uni</li>
</country>
<region><li>Grand Est</li>
<li>Lorraine (région)</li>
<li>Écosse</li>
</region>
<settlement><li>Glasgow</li>
<li>Vandœuvre-lès-Nancy</li>
</settlement>
<orgName><li>Université de Glasgow</li>
</orgName>
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<tree><noCountry><name sortKey="Mavridis, Lazaros" sort="Mavridis, Lazaros" uniqKey="Mavridis L" first="Lazaros" last="Mavridis">Lazaros Mavridis</name>
<name sortKey="Ritchie, David W" sort="Ritchie, David W" uniqKey="Ritchie D" first="David W." last="Ritchie">David W. Ritchie</name>
<name sortKey="Venkatraman, Vishwesh" sort="Venkatraman, Vishwesh" uniqKey="Venkatraman V" first="Vishwesh" last="Venkatraman">Vishwesh Venkatraman</name>
</noCountry>
<country name="Royaume-Uni"><region name="Écosse"><name sortKey="Macindoe, Gary" sort="Macindoe, Gary" uniqKey="Macindoe G" first="Gary" last="Macindoe">Gary Macindoe</name>
</region>
</country>
<country name="France"><region name="Grand Est"><name sortKey="Devignes, Marie Dominique" sort="Devignes, Marie Dominique" uniqKey="Devignes M" first="Marie-Dominique" last="Devignes">Marie-Dominique Devignes</name>
</region>
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</record>

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HexServer: an FFT-based protein docking server powered by graphics processors

HexServer: an FFT-based protein docking server powered by graphics processors

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Abstract

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