A grid-enabled web service for low-resolution crystal structure refinement
Identifieur interne : 000286 ( Ncbi/Merge ); précédent : 000285; suivant : 000287A grid-enabled web service for low-resolution crystal structure refinement
Auteurs : Daniel J. O Onovan [États-Unis] ; Ian Stokes-Rees [États-Unis] ; Yunsun Nam [États-Unis] ; Stephen C. Blacklow [États-Unis] ; Gunnar F. Schröder [Allemagne] ; Axel T. Brunger [États-Unis] ; Piotr Sliz [États-Unis]Source :
- Acta Crystallographica Section D: Biological Crystallography [ 0907-4449 ] ; 2012.
English descriptors
- KwdEn :
- MESH :
Abstract
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.
Url:
DOI: 10.1107/S0907444912001163
PubMed: 22349228
PubMed Central: 3282622
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PMC:3282622Le document en format XML
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<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>
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<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
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<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
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, 52425 Jülich,<country>Germany</country>
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<country xml:lang="fr">Allemagne</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
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, J. H. Clark Center E300C, 318 Campus Drive, Stanford, CA 94305,<country>USA</country>
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<country xml:lang="fr">États-Unis</country>
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<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>
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<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>
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<pubmed><TEI><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>
<affiliation wicri:level="2"><nlm:affiliation>Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115</wicri:regionArea>
<placeName><region type="state">Massachusetts</region>
</placeName>
</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>
</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>
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<date when="2012">2012</date>
<idno type="doi">10.1107/S0907444912001163</idno>
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<sourceDesc><biblStruct><analytic><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>
<affiliation wicri:level="2"><nlm:affiliation>Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115</wicri:regionArea>
<placeName><region type="state">Massachusetts</region>
</placeName>
</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>
</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>
<series><title level="j">Acta crystallographica. Section D, Biological crystallography</title>
<idno type="eISSN">1399-0047</idno>
<imprint><date when="2012" type="published">2012</date>
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<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>
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<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>
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