Developing science gateways for drug discovery in a grid environment
Identifieur interne : 000191 ( Pmc/Curation ); précédent : 000190; suivant : 000192Developing science gateways for drug discovery in a grid environment
Auteurs : Horacio Pérez-Sánchez [Espagne] ; Vahid Rezaei [Iran] ; Vitaliy Mezhuyev [Malaisie] ; Duhu Man [République populaire de Chine] ; Jorge Pe A-García [Espagne] ; Helena Den-Haan [Espagne] ; Sandra Gesing [États-Unis]Source :
- SpringerPlus [ 2193-1801 ] ; 2016.
Abstract
Methods for in silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide the research community of life sciences with a convenient tool for high-throughput virtual screening on distributed computing resources.
To this end, we recently integrated the biophysics-based drug-screening program FlexScreen into a service, applicable for large-scale parallel screening and reusable in the context of scientific workflows.
Our implementation is based on Pipeline Pilot and Simple Object Access Protocol and provides an easy-to-use graphical user interface to construct complex workflows, which can be executed on distributed computing resources, thus accelerating the throughput by several orders of magnitude.
Url:
DOI: 10.1186/s40064-016-2914-x
PubMed: 27547674
PubMed Central: 4978646
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Faculty of Mathematics and Computer Sciences, Allameh Tabataba’i University, Tehran, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea> Department of Statistics, Faculty of Mathematics and Computer Sciences, Allameh Tabataba’i University, Tehran</wicri:regionArea></affiliation></author><author><name sortKey="Mezhuyev, Vitaliy" sort="Mezhuyev, Vitaliy" uniqKey="Mezhuyev V" first="Vitaliy" last="Mezhuyev">Vitaliy Mezhuyev</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Faculty of Computer Systems and Software Engineering, University Malaysia Pahang, Pekan, Malaysia</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Faculty of Computer Systems and Software Engineering, University Malaysia Pahang, Pekan</wicri:regionArea></affiliation></author><author><name sortKey="Man, Duhu" sort="Man, Duhu" uniqKey="Man D" first="Duhu" last="Man">Duhu Man</name><affiliation wicri:level="1"><nlm:aff id="Aff4">Shenzhen Institutes of Advanced Technologies, Chinese 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last="Den-Haan">Helena Den-Haan</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Catolica San Antonio de Murcia (UCAM), Murcia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Catolica San Antonio de Murcia (UCAM), Murcia</wicri:regionArea></affiliation></author><author><name sortKey="Gesing, Sandra" sort="Gesing, Sandra" uniqKey="Gesing S" first="Sandra" last="Gesing">Sandra Gesing</name><affiliation wicri:level="2"><nlm:aff id="Aff5">Center for Research Computing, University of Notre Dame, Notre Dame, IN USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Indiana</region></placeName><wicri:cityArea>Center for Research Computing, University of Notre Dame, Notre Dame</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27547674</idno><idno type="pmc">4978646</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978646</idno><idno type="RBID">PMC:4978646</idno><idno type="doi">10.1186/s40064-016-2914-x</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000191</idno><idno type="wicri:Area/Pmc/Curation">000191</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Developing science gateways for drug discovery in a grid environment</title><author><name sortKey="Perez Sanchez, Horacio" sort="Perez Sanchez, Horacio" uniqKey="Perez Sanchez H" first="Horacio" last="Pérez-Sánchez">Horacio Pérez-Sánchez</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Catolica San Antonio de Murcia (UCAM), Murcia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Catolica San Antonio de Murcia (UCAM), Murcia</wicri:regionArea></affiliation></author><author><name sortKey="Rezaei, Vahid" sort="Rezaei, Vahid" uniqKey="Rezaei V" first="Vahid" last="Rezaei">Vahid Rezaei</name><affiliation wicri:level="1"><nlm:aff id="Aff2"> Department of Statistics, Faculty of Mathematics and Computer Sciences, Allameh Tabataba’i University, Tehran, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea> Department of Statistics, Faculty of Mathematics and Computer Sciences, Allameh Tabataba’i University, Tehran</wicri:regionArea></affiliation></author><author><name sortKey="Mezhuyev, Vitaliy" sort="Mezhuyev, Vitaliy" uniqKey="Mezhuyev V" first="Vitaliy" last="Mezhuyev">Vitaliy Mezhuyev</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Faculty of Computer Systems and Software Engineering, University Malaysia Pahang, Pekan, Malaysia</nlm:aff><country xml:lang="fr">Malaisie</country><wicri:regionArea>Faculty of Computer Systems and Software Engineering, University Malaysia Pahang, Pekan</wicri:regionArea></affiliation></author><author><name sortKey="Man, Duhu" sort="Man, Duhu" uniqKey="Man D" first="Duhu" last="Man">Duhu Man</name><affiliation wicri:level="1"><nlm:aff id="Aff4">Shenzhen Institutes of Advanced Technologies, Chinese Academy of Sciences, Shenzhen, P.R.China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shenzhen Institutes of Advanced Technologies, Chinese Academy of Sciences, Shenzhen</wicri:regionArea></affiliation></author><author><name sortKey="Pe A Garcia, Jorge" sort="Pe A Garcia, Jorge" uniqKey="Pe A Garcia J" first="Jorge" last="Pe A-García">Jorge Pe A-García</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Catolica San Antonio de Murcia (UCAM), Murcia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Catolica San Antonio de Murcia (UCAM), Murcia</wicri:regionArea></affiliation></author><author><name sortKey="Den Haan, Helena" sort="Den Haan, Helena" uniqKey="Den Haan H" first="Helena" last="Den-Haan">Helena Den-Haan</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Catolica San Antonio de Murcia (UCAM), Murcia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Catolica San Antonio de Murcia (UCAM), Murcia</wicri:regionArea></affiliation></author><author><name sortKey="Gesing, Sandra" sort="Gesing, Sandra" uniqKey="Gesing S" first="Sandra" last="Gesing">Sandra Gesing</name><affiliation wicri:level="2"><nlm:aff id="Aff5">Center for Research Computing, University of Notre Dame, Notre Dame, IN USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Indiana</region></placeName><wicri:cityArea>Center for Research Computing, University of Notre Dame, Notre Dame</wicri:cityArea></affiliation></author></analytic><series><title level="j">SpringerPlus</title><idno type="eISSN">2193-1801</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Methods for in silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide the research community of life sciences with a convenient tool for high-throughput virtual screening on distributed computing resources.</p></sec><sec><title>Results</title><p>To this end, we recently integrated the biophysics-based drug-screening program FlexScreen into a service, applicable for large-scale parallel screening and reusable in the context of scientific workflows.</p></sec><sec><title>Conclusions</title><p>Our implementation is based on Pipeline Pilot and Simple Object Access Protocol and provides an easy-to-use graphical user interface to construct complex workflows, which can be executed on distributed computing resources, thus accelerating the throughput by several orders of magnitude.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Berthold, M" uniqKey="Berthold M">M 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Springerplus</journal-id><journal-id journal-id-type="iso-abbrev">Springerplus</journal-id><journal-title-group><journal-title>SpringerPlus</journal-title></journal-title-group><issn pub-type="epub">2193-1801</issn><publisher><publisher-name>Springer International Publishing</publisher-name><publisher-loc>Cham</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27547674</article-id><article-id pub-id-type="pmc">4978646</article-id><article-id pub-id-type="publisher-id">2914</article-id><article-id pub-id-type="doi">10.1186/s40064-016-2914-x</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research</subject></subj-group></article-categories><title-group><article-title>Developing science gateways for drug discovery in a grid environment</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name><surname>Pérez-Sánchez</surname><given-names>Horacio</given-names></name><address><email>hperez@ucam.edu</email></address><xref ref-type="aff" rid="Aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Rezaei</surname><given-names>Vahid</given-names></name><address><email>vhrezaei@gmail.com</email></address><xref ref-type="aff" rid="Aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Mezhuyev</surname><given-names>Vitaliy</given-names></name><address><email>mejuev@ukr.net</email></address><xref ref-type="aff" rid="Aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Man</surname><given-names>Duhu</given-names></name><address><email>dh.man@siat.ac.cn</email></address><xref ref-type="aff" rid="Aff4">4</xref></contrib><contrib contrib-type="author"><name><surname>Peña-García</surname><given-names>Jorge</given-names></name><address><email>jpena@ucam.edu</email></address><xref ref-type="aff" rid="Aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>den-Haan</surname><given-names>Helena</given-names></name><address><email>hden@alu.ucam.edu</email></address><xref ref-type="aff" rid="Aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Gesing</surname><given-names>Sandra</given-names></name><address><email>sandra.gesing@nd.edu</email></address><xref ref-type="aff" rid="Aff5">5</xref></contrib><aff id="Aff1"><label>1</label>Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Catolica San Antonio de Murcia (UCAM), Murcia, Spain</aff><aff id="Aff2"><label>2</label> Department of Statistics, Faculty of Mathematics and Computer Sciences, Allameh Tabataba’i University, Tehran, Iran</aff><aff id="Aff3"><label>3</label>Faculty of Computer Systems and Software Engineering, University Malaysia Pahang, Pekan, Malaysia</aff><aff id="Aff4"><label>4</label>Shenzhen Institutes of Advanced Technologies, Chinese Academy of Sciences, Shenzhen, P.R.China</aff><aff id="Aff5"><label>5</label>Center for Research Computing, University of Notre Dame, Notre Dame, IN USA</aff></contrib-group><pub-date pub-type="epub"><day>9</day><month>8</month><year>2016</year></pub-date><pub-date pub-type="pmc-release"><day>9</day><month>8</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>5</volume><issue>1</issue><elocation-id>1300</elocation-id><history><date date-type="received"><day>21</day><month>3</month><year>2016</year></date><date date-type="accepted"><day>26</day><month>7</month><year>2016</year></date></history><permissions><copyright-statement>© The Author(s) 2016</copyright-statement><license license-type="OpenAccess"><license-p><bold>Open Access</bold>This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.</license-p></license></permissions><abstract id="Abs1"><sec><title>Background</title><p>Methods for in silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide the research community of life sciences with a convenient tool for high-throughput virtual screening on distributed computing resources.</p></sec><sec><title>Results</title><p>To this end, we recently integrated the biophysics-based drug-screening program FlexScreen into a service, applicable for large-scale parallel screening and reusable in the context of scientific workflows.</p></sec><sec><title>Conclusions</title><p>Our implementation is based on Pipeline Pilot and Simple Object Access Protocol and provides an easy-to-use graphical user interface to construct complex workflows, which can be executed on distributed computing resources, thus accelerating the throughput by several orders of magnitude.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>Virtual screening</kwd><kwd>FlexScreen</kwd><kwd>Science gateways</kwd><kwd>Drug discovery</kwd><kwd>High performance computing</kwd></kwd-group><funding-group><award-group><funding-source><institution>Fundación Séneca (ES)</institution></funding-source><award-id>18946/JLI/13</award-id><principal-award-recipient><name><surname>Pérez-Sánchez</surname><given-names>Horacio</given-names></name></principal-award-recipient></award-group></funding-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2016</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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