CyberinfraV1, PubMed, Corpus, bibRecord, 000032

A grid-enabled web service for low-resolution crystal structure refinement.

Identifieur interne : 000032 ( PubMed/Corpus ); précédent : 000031; suivant : 000033

A 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 Sliz

Source :

Acta crystallographica. Section D, Biological crystallography [ 1399-0047 ] ; 2012.

RBID : pubmed:22349228

English descriptors

KwdEn :
- Computational Biology (methods), Computer Systems, Crystallography, X-Ray (methods), Internet, Software, User-Computer Interface.
MESH :
- methods : Computational Biology, Crystallography, X-Ray.
- Computer Systems, Internet, Software, User-Computer Interface.

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.

DOI: 10.1107/S0907444912001163
PubMed: 22349228

Links to Exploration step

pubmed:22349228

Le document en format XML

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<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><nlm:affiliation>Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.</nlm:affiliation>
</affiliation>
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<author><name sortKey="Stokes Rees, Ian" sort="Stokes Rees, Ian" uniqKey="Stokes Rees I" first="Ian" last="Stokes-Rees">Ian Stokes-Rees</name>
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<author><name sortKey="Nam, Yunsun" sort="Nam, Yunsun" uniqKey="Nam Y" first="Yunsun" last="Nam">Yunsun Nam</name>
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<author><name sortKey="Brunger, Axel T" sort="Brunger, Axel T" uniqKey="Brunger A" first="Axel T" last="Brunger">Axel T. Brunger</name>
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<author><name sortKey="Sliz, Piotr" sort="Sliz, Piotr" uniqKey="Sliz P" first="Piotr" last="Sliz">Piotr Sliz</name>
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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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<CommentsCorrections RefType="Cites"><RefSource>Nature. 2010 Apr 22;464(7292):1218-22</RefSource>
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<CommentsCorrections RefType="Cites"><RefSource>Cell. 2006 Mar 10;124(5):985-96</RefSource>
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<CommentsCorrections RefType="Cites"><RefSource>Structure. 2012 Feb 8;20(2):340-9</RefSource>
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<CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2000 Jan 1;28(1):235-42</RefSource>
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<CommentsCorrections RefType="Cites"><RefSource>Cell. 2006 Mar 10;124(5):973-83</RefSource>
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<CommentsCorrections RefType="Cites"><RefSource>Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21476-81</RefSource>
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A grid-enabled web service for low-resolution crystal structure refinement.

A grid-enabled web service for low-resolution crystal structure refinement.

Source :

English descriptors

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki