A grid‐enabled web service for low‐resolution crystal structure refinement
Identifieur interne : 000622 ( Main/Merge ); précédent : 000621; suivant : 000623A grid‐enabled web service for low‐resolution crystal structure refinement
Auteurs : Daniel J. O'Donovan ; Ian Stokes-Rees ; Yunsun Nam ; Stephen C. Blacklow ; Gunnar F. Schröder ; Axel T. Brunger ; Piotr SlizSource :
- Acta Crystallographica Section D [ 1399-0047 ] ; 2012-03-01.
English descriptors
- KwdEn :
- MESH :
Abstract
Deformable elastic network (DEN) restraints have proved to be a powerful tool for refining structures from low‐resolution X‐ray crystallographic data sets. Unfortunately, optimal refinement using DEN restraints requires extensive calculations and is often hindered by a lack of access to sufficient computational resources. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements in parallel on the Open Science Grid, the US cyberinfrastructure. Access to the grid is provided through a simple and intuitive web interface integrated into the SBGrid Science Portal. Using this portal, refinements combined with full parameter optimization that would take many thousands of hours on standard computational resources can now be completed in several hours. An example of the successful application of DEN restraints to the human Notch1 transcriptional complex using the grid resource, and summaries of all submitted refinements, are presented as justification.
Url:
- https://api.istex.fr/document/B5A52C8281B22EAA5CDB906FC6548E7C1C203DEE/fulltext/pdf
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3282622
DOI: 10.1107/S0907444912001163
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O'Donovan</name></author><author><name sortKey="Stokes Ees, Ian" sort="Stokes Ees, Ian" uniqKey="Stokes Ees I" first="Ian" last="Stokes-Rees">Ian Stokes-Rees</name></author><author><name sortKey="Nam, Yunsun" sort="Nam, Yunsun" uniqKey="Nam Y" first="Yunsun" last="Nam">Yunsun Nam</name></author><author><name sortKey="Blacklow, Stephen C" sort="Blacklow, Stephen C" uniqKey="Blacklow S" first="Stephen C." last="Blacklow">Stephen C. Blacklow</name></author><author><name sortKey="Schroder, Gunnar F" sort="Schroder, Gunnar F" uniqKey="Schroder G" first="Gunnar F." last="Schröder">Gunnar F. Schröder</name></author><author><name sortKey="Brunger, Axel T" sort="Brunger, Axel T" uniqKey="Brunger A" first="Axel T." last="Brunger">Axel T. Brunger</name></author><author><name sortKey="Sliz, Piotr" sort="Sliz, Piotr" uniqKey="Sliz P" first="Piotr" last="Sliz">Piotr Sliz</name></author></analytic><monogr></monogr><series><title level="j">Acta Crystallographica Section D</title><title level="j" type="abbrev">Acta Cryst. D</title><idno type="ISSN">1399-0047</idno><idno type="eISSN">1399-0047</idno><imprint><publisher>International Union of Crystallography</publisher><pubPlace>5 Abbey Square, Chester, Cheshire CH1 2HU, England</pubPlace><date type="published" when="2012-03-01">2012-03-01</date><biblScope unit="volume">68</biblScope><biblScope unit="issue">3</biblScope><biblScope unit="page" from="261">261</biblScope><biblScope unit="page" to="267">267</biblScope></imprint><idno type="ISSN">1399-0047</idno></series><idno type="istex">B5A52C8281B22EAA5CDB906FC6548E7C1C203DEE</idno><idno type="DOI">10.1107/S0907444912001163</idno><idno type="ArticleID">AYDDZ5246</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1399-0047</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (methods)</term><term>Computer Systems</term><term>Crystallography, X-Ray (methods)</term><term>DEN refinement</term><term>Internet</term><term>Software</term><term>User-Computer Interface</term><term>deformable elastic network restraints</term><term>low‐resolution refinement</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Crystallography, X-Ray</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Systems</term><term>Internet</term><term>Software</term><term>User-Computer Interface</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Deformable elastic network (DEN) restraints have proved to be a powerful tool for refining structures from low‐resolution X‐ray crystallographic data sets. Unfortunately, optimal refinement using DEN restraints requires extensive calculations and is often hindered by a lack of access to sufficient computational resources. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements in parallel on the Open Science Grid, the US cyberinfrastructure. Access to the grid is provided through a simple and intuitive web interface integrated into the SBGrid Science Portal. Using this portal, refinements combined with full parameter optimization that would take many thousands of hours on standard computational resources can now be completed in several hours. An example of the successful application of DEN restraints to the human Notch1 transcriptional complex using the grid resource, and summaries of all submitted refinements, are presented as justification.</div></front></TEI><double doi="10.1107/S0907444912001163"><ISTEX><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">A grid‐enabled web service for low‐resolution crystal structure refinement</title><author><name sortKey="O Donovan, Daniel J" sort="O Donovan, Daniel J" uniqKey="O Donovan D" first="Daniel J." last="O'Donovan">Daniel J. O'Donovan</name></author><author><name sortKey="Stokes Ees, Ian" sort="Stokes Ees, Ian" uniqKey="Stokes Ees I" first="Ian" last="Stokes-Rees">Ian Stokes-Rees</name></author><author><name sortKey="Nam, Yunsun" sort="Nam, Yunsun" uniqKey="Nam Y" first="Yunsun" last="Nam">Yunsun Nam</name></author><author><name sortKey="Blacklow, Stephen C" sort="Blacklow, Stephen C" uniqKey="Blacklow S" first="Stephen C." last="Blacklow">Stephen C. Blacklow</name></author><author><name sortKey="Schroder, Gunnar F" sort="Schroder, Gunnar F" uniqKey="Schroder G" first="Gunnar F." last="Schröder">Gunnar F. Schröder</name></author><author><name sortKey="Brunger, Axel T" sort="Brunger, Axel T" uniqKey="Brunger A" first="Axel T." last="Brunger">Axel T. 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O'Donovan</name></author><author><name sortKey="Stokes Ees, Ian" sort="Stokes Ees, Ian" uniqKey="Stokes Ees I" first="Ian" last="Stokes-Rees">Ian Stokes-Rees</name></author><author><name sortKey="Nam, Yunsun" sort="Nam, Yunsun" uniqKey="Nam Y" first="Yunsun" last="Nam">Yunsun Nam</name></author><author><name sortKey="Blacklow, Stephen C" sort="Blacklow, Stephen C" uniqKey="Blacklow S" first="Stephen C." last="Blacklow">Stephen C. Blacklow</name></author><author><name sortKey="Schroder, Gunnar F" sort="Schroder, Gunnar F" uniqKey="Schroder G" first="Gunnar F." last="Schröder">Gunnar F. Schröder</name></author><author><name sortKey="Brunger, Axel T" sort="Brunger, Axel T" uniqKey="Brunger A" first="Axel T." last="Brunger">Axel T. Brunger</name></author><author><name sortKey="Sliz, Piotr" sort="Sliz, Piotr" uniqKey="Sliz P" first="Piotr" last="Sliz">Piotr Sliz</name></author></analytic><monogr></monogr><series><title level="j">Acta Crystallographica Section D</title><title level="j" type="abbrev">Acta Cryst. D</title><idno type="ISSN">1399-0047</idno><idno type="eISSN">1399-0047</idno><imprint><publisher>International Union of Crystallography</publisher><pubPlace>5 Abbey Square, Chester, Cheshire CH1 2HU, England</pubPlace><date type="published" when="2012-03-01">2012-03-01</date><biblScope unit="volume">68</biblScope><biblScope unit="issue">3</biblScope><biblScope unit="page" from="261">261</biblScope><biblScope unit="page" to="267">267</biblScope></imprint><idno type="ISSN">1399-0047</idno></series><idno type="istex">B5A52C8281B22EAA5CDB906FC6548E7C1C203DEE</idno><idno type="DOI">10.1107/S0907444912001163</idno><idno type="ArticleID">AYDDZ5246</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1399-0047</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DEN refinement</term><term>deformable elastic network restraints</term><term>low‐resolution refinement</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Deformable elastic network (DEN) restraints have proved to be a powerful tool for refining structures from low‐resolution X‐ray crystallographic data sets. Unfortunately, optimal refinement using DEN restraints requires extensive calculations and is often hindered by a lack of access to sufficient computational resources. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements in parallel on the Open Science Grid, the US cyberinfrastructure. Access to the grid is provided through a simple and intuitive web interface integrated into the SBGrid Science Portal. Using this portal, refinements combined with full parameter optimization that would take many thousands of hours on standard computational resources can now be completed in several hours. An example of the successful application of DEN restraints to the human Notch1 transcriptional complex using the grid resource, and summaries of all submitted refinements, are presented as justification.</div></front></TEI></ISTEX><PMC><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A grid-enabled web service for low-resolution crystal structure refinement</title><author><name sortKey="O Onovan, Daniel J" sort="O Onovan, Daniel J" uniqKey="O Onovan D" first="Daniel J." last="O Onovan">Daniel J. O Onovan</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Stokes Rees, Ian" sort="Stokes Rees, Ian" uniqKey="Stokes Rees I" first="Ian" last="Stokes-Rees">Ian Stokes-Rees</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Nam, Yunsun" sort="Nam, Yunsun" uniqKey="Nam Y" first="Yunsun" last="Nam">Yunsun Nam</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Blacklow, Stephen C" sort="Blacklow, Stephen C" uniqKey="Blacklow S" first="Stephen C." last="Blacklow">Stephen C. Blacklow</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="b">Department of Cancer Biology,<institution>Dana Farber Cancer Institute</institution>, Boston, MA 02215,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="c">Department of Pathology,<institution>Brigham and Women’s Hospital</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Schroder, Gunnar F" sort="Schroder, Gunnar F" uniqKey="Schroder G" first="Gunnar F." last="Schröder">Gunnar F. Schröder</name><affiliation wicri:level="1"><nlm:aff id="d">Forschungszentrum Jülich,<institution>Institute of Complex Systems (ICS-6)</institution>, 52425 Jülich,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Brunger, Axel T" sort="Brunger, Axel T" uniqKey="Brunger A" first="Axel T." last="Brunger">Axel T. Brunger</name><affiliation wicri:level="1"><nlm:aff id="e">Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science,<institution>Stanford School of Medicine</institution>, J. H. Clark Center E300C, 318 Campus Drive, Stanford, CA 94305,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Sliz, Piotr" sort="Sliz, Piotr" uniqKey="Sliz P" first="Piotr" last="Sliz">Piotr Sliz</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="f">Laboratory of Molecular Medicine,<institution>Children’s Hospital</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22349228</idno><idno type="pmc">3282622</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3282622</idno><idno type="RBID">PMC:3282622</idno><idno type="doi">10.1107/S0907444912001163</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000474</idno><idno type="wicri:Area/Pmc/Curation">000474</idno><idno type="wicri:Area/Pmc/Checkpoint">000445</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">000032</idno><idno type="wicri:Area/PubMed/Curation">000032</idno><idno type="wicri:Area/PubMed/Checkpoint">000032</idno><idno type="wicri:Area/Ncbi/Merge">000286</idno><idno type="wicri:Area/Ncbi/Curation">000286</idno><idno type="wicri:Area/Ncbi/Checkpoint">000286</idno><idno type="wicri:doubleKey">0907-4449:2012:O Onovan D:a:grid:enabled</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A grid-enabled web service for low-resolution crystal structure refinement</title><author><name sortKey="O Onovan, Daniel J" sort="O Onovan, Daniel J" uniqKey="O Onovan D" first="Daniel J." last="O Onovan">Daniel J. O Onovan</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Stokes Rees, Ian" sort="Stokes Rees, Ian" uniqKey="Stokes Rees I" first="Ian" last="Stokes-Rees">Ian Stokes-Rees</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Nam, Yunsun" sort="Nam, Yunsun" uniqKey="Nam Y" first="Yunsun" last="Nam">Yunsun Nam</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Blacklow, Stephen C" sort="Blacklow, Stephen C" uniqKey="Blacklow S" first="Stephen C." last="Blacklow">Stephen C. Blacklow</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="b">Department of Cancer Biology,<institution>Dana Farber Cancer Institute</institution>, Boston, MA 02215,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="c">Department of Pathology,<institution>Brigham and Women’s Hospital</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Schroder, Gunnar F" sort="Schroder, Gunnar F" uniqKey="Schroder G" first="Gunnar F." last="Schröder">Gunnar F. Schröder</name><affiliation wicri:level="1"><nlm:aff id="d">Forschungszentrum Jülich,<institution>Institute of Complex Systems (ICS-6)</institution>, 52425 Jülich,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Brunger, Axel T" sort="Brunger, Axel T" uniqKey="Brunger A" first="Axel T." last="Brunger">Axel T. Brunger</name><affiliation wicri:level="1"><nlm:aff id="e">Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science,<institution>Stanford School of Medicine</institution>, J. H. Clark Center E300C, 318 Campus Drive, Stanford, CA 94305,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Sliz, Piotr" sort="Sliz, Piotr" uniqKey="Sliz P" first="Piotr" last="Sliz">Piotr Sliz</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="f">Laboratory of Molecular Medicine,<institution>Children’s Hospital</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Acta Crystallographica Section D: Biological Crystallography</title><idno type="ISSN">0907-4449</idno><idno type="eISSN">1399-0047</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (methods)</term><term>Computer Systems</term><term>Crystallography, X-Ray (methods)</term><term>Internet</term><term>Software</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Crystallography, X-Ray</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Systems</term><term>Internet</term><term>Software</term><term>User-Computer Interface</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The deformable elastic network (DEN) method for reciprocal-space crystallographic refinement improves crystal structures, especially at resolutions lower than 3.5 Å. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI></PMC></double></record>Pour manipuler ce document sous Unix (Dilib)
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