CyberinfraV1, Main, Exploration, bibRecord, 000621

A grid‐enabled web service for low‐resolution crystal structure refinement

Identifieur interne : 000621 ( Main/Exploration ); précédent : 000620; suivant : 000622

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 [ 1399-0047 ] ; 2012-03-01.

RBID : ISTEX:B5A52C8281B22EAA5CDB906FC6548E7C1C203DEE

English descriptors

KwdEn :
- Computational Biology (methods), Computer Systems, Crystallography, X-Ray (methods), DEN refinement, Internet, Software, User-Computer Interface, deformable elastic network restraints, low‐resolution refinement.
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.

Url:

DOI: 10.1107/S0907444912001163

Affiliations:

Le document en format XML

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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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A grid‐enabled web service for low‐resolution crystal structure refinement

A grid‐enabled web service for low‐resolution crystal structure refinement

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English descriptors

Abstract

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