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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Design of a Grid Service-based Platform for In Silico Protein-Ligand Screenings</title><author><name sortKey="Levesque, Marshall J" sort="Levesque, Marshall J" uniqKey="Levesque M" first="Marshall J." last="Levesque">Marshall J. Levesque</name><affiliation><nlm:aff id="A3"> Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA, 92093-0435</nlm:aff></affiliation></author><author><name sortKey="Ichikawa, Kohei" sort="Ichikawa, Kohei" uniqKey="Ichikawa K" first="Kohei" last="Ichikawa">Kohei Ichikawa</name><affiliation><nlm:aff id="A2"> Research Center of Socionetwork Strategies, The Institution of Economic and Political Studies, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka, 564-8680 Japan</nlm:aff></affiliation></author><author><name sortKey="Date, Susumu" sort="Date, Susumu" uniqKey="Date S" first="Susumu" last="Date">Susumu Date</name><affiliation><nlm:aff id="A1"> Cybermedia Center, Osaka University, 5-1 Mihogaoka Ibaraki, Osaka 567-0047, Japan</nlm:aff></affiliation></author><author><name sortKey="Haga, Jason H" sort="Haga, Jason H" uniqKey="Haga J" first="Jason H." last="Haga">Jason H. Haga</name><affiliation><nlm:aff id="A3"> Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA, 92093-0435</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18771812</idno><idno type="pmc">2665129</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665129</idno><idno type="RBID">PMC:2665129</idno><idno type="doi">10.1016/j.cmpb.2008.07.005</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">000298</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Design of a Grid Service-based Platform for In Silico Protein-Ligand Screenings</title><author><name sortKey="Levesque, Marshall J" sort="Levesque, Marshall J" uniqKey="Levesque M" first="Marshall J." last="Levesque">Marshall J. Levesque</name><affiliation><nlm:aff id="A3"> Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA, 92093-0435</nlm:aff></affiliation></author><author><name sortKey="Ichikawa, Kohei" sort="Ichikawa, Kohei" uniqKey="Ichikawa K" first="Kohei" last="Ichikawa">Kohei Ichikawa</name><affiliation><nlm:aff id="A2"> Research Center of Socionetwork Strategies, The Institution of Economic and Political Studies, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka, 564-8680 Japan</nlm:aff></affiliation></author><author><name sortKey="Date, Susumu" sort="Date, Susumu" uniqKey="Date S" first="Susumu" last="Date">Susumu Date</name><affiliation><nlm:aff id="A1"> Cybermedia Center, Osaka University, 5-1 Mihogaoka Ibaraki, Osaka 567-0047, Japan</nlm:aff></affiliation></author><author><name sortKey="Haga, Jason H" sort="Haga, Jason H" uniqKey="Haga J" first="Jason H." last="Haga">Jason H. Haga</name><affiliation><nlm:aff id="A3"> Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA, 92093-0435</nlm:aff></affiliation></author></analytic><series><title level="j">Computer methods and programs in biomedicine</title><idno type="ISSN">0169-2607</idno><idno type="eISSN">1872-7565</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">Grid computing offers the powerful alternative of sharing resources on a worldwide scale, across different institutions to run computationally intensive, scientific applications without the need for a centralized supercomputer. Much effort has been put into development of software that deploys legacy applications on a grid-based infrastructure and efficiently uses available resources. One field that can benefit greatly from the use of grid resources is that of drug discovery since molecular docking simulations are an integral part of the discovery process. In this paper, we present a scalable, reusable platform to choreograph large virtual screening experiments over a computational grid using the molecular docking simulation software DOCK. Software components are applied on multiple levels to create automated workflows consisting of input data delivery, job scheduling, status query, and collection of output to be displayed in a manageable fashion for further analysis. This was achieved using Opal OP to wrap the DOCK application as a grid service and PERL for data manipulation purposes, alleviating the requirement for extensive knowledge of grid infrastructure. With the platform in place, a screening of the ZINC 2,066,906 compound “druglike” subset database against an enzyme's catalytic site was successfully performed using the MPI version of DOCK 5.4 on the PRAGMA grid testbed. The screening required 11.56 days laboratory time and utilized 200 processors over 7 clusters.</p></div></front></TEI><pmc article-type="research-article" xml:lang="EN"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">8506513</journal-id><journal-id journal-id-type="pubmed-jr-id">3134</journal-id><journal-id journal-id-type="nlm-ta">Comput Methods Programs Biomed</journal-id><journal-title>Computer methods and programs in biomedicine</journal-title><issn pub-type="ppub">0169-2607</issn><issn pub-type="epub">1872-7565</issn></journal-meta><article-meta><article-id pub-id-type="pmid">18771812</article-id><article-id pub-id-type="pmc">2665129</article-id><article-id pub-id-type="doi">10.1016/j.cmpb.2008.07.005</article-id><article-id pub-id-type="manuscript">NIHMS92120</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Design of a Grid Service-based Platform for In Silico Protein-Ligand Screenings</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Levesque</surname><given-names>Marshall J.</given-names></name><xref rid="A3" ref-type="aff">3</xref></contrib><contrib contrib-type="author"><name><surname>Ichikawa</surname><given-names>Kohei</given-names></name><xref rid="A2" ref-type="aff">2</xref></contrib><contrib contrib-type="author"><name><surname>Date</surname><given-names>Susumu</given-names></name><xref rid="A1" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Haga</surname><given-names>Jason H.</given-names></name><xref rid="A3" ref-type="aff">3</xref></contrib></contrib-group><aff id="A1"><label>1</label> Cybermedia Center, Osaka University, 5-1 Mihogaoka Ibaraki, Osaka 567-0047, Japan</aff><aff id="A2"><label>2</label> Research Center of Socionetwork Strategies, The Institution of Economic and Political Studies, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka, 564-8680 Japan</aff><aff id="A3"><label>3</label> Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA, 92093-0435</aff><author-notes><corresp id="FN1">To whom correspondence should be addressed: Jason H. Haga, Ph.D., Department of Bioengineering, MC: 0435, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0435, Phone: 858-534-3399, FAX: 858-822-1160, Email: <email>jhaga@bioeng.ucsd.edu</email></corresp></author-notes><pub-date pub-type="nihms-submitted"><day>25</day><month>2</month><year>2009</year></pub-date><pub-date pub-type="epub"><day>3</day><month>9</month><year>2008</year></pub-date><pub-date pub-type="ppub"><month>1</month><year>2009</year></pub-date><pub-date pub-type="pmc-release"><day>1</day><month>1</month><year>2010</year></pub-date><volume>93</volume><issue>1</issue><fpage>73</fpage><lpage>82</lpage><abstract><p id="P1">Grid computing offers the powerful alternative of sharing resources on a worldwide scale, across different institutions to run computationally intensive, scientific applications without the need for a centralized supercomputer. Much effort has been put into development of software that deploys legacy applications on a grid-based infrastructure and efficiently uses available resources. One field that can benefit greatly from the use of grid resources is that of drug discovery since molecular docking simulations are an integral part of the discovery process. In this paper, we present a scalable, reusable platform to choreograph large virtual screening experiments over a computational grid using the molecular docking simulation software DOCK. Software components are applied on multiple levels to create automated workflows consisting of input data delivery, job scheduling, status query, and collection of output to be displayed in a manageable fashion for further analysis. This was achieved using Opal OP to wrap the DOCK application as a grid service and PERL for data manipulation purposes, alleviating the requirement for extensive knowledge of grid infrastructure. With the platform in place, a screening of the ZINC 2,066,906 compound “druglike” subset database against an enzyme's catalytic site was successfully performed using the MPI version of DOCK 5.4 on the PRAGMA grid testbed. The screening required 11.56 days laboratory time and utilized 200 processors over 7 clusters.</p></abstract><kwd-group><kwd>Grid computing</kwd><kwd>virtual screening</kwd><kwd>molecular simulation</kwd><kwd>DOCK</kwd><kwd>Opal OP</kwd></kwd-group><contract-num rid="HL1">R01 HL085159-03</contract-num><contract-sponsor id="HL1">National Heart, Lung, and Blood Institute : NHLBI</contract-sponsor></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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