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

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 c...

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Autores principales: O’Donovan, Daniel J., Stokes-Rees, Ian, Nam, Yunsun, Blacklow, Stephen C., Schröder, Gunnar F., Brunger, Axel T., Sliz, Piotr
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3282622/
https://www.ncbi.nlm.nih.gov/pubmed/22349228
http://dx.doi.org/10.1107/S0907444912001163
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author O’Donovan, Daniel J.
Stokes-Rees, Ian
Nam, Yunsun
Blacklow, Stephen C.
Schröder, Gunnar F.
Brunger, Axel T.
Sliz, Piotr
author_facet O’Donovan, Daniel J.
Stokes-Rees, Ian
Nam, Yunsun
Blacklow, Stephen C.
Schröder, Gunnar F.
Brunger, Axel T.
Sliz, Piotr
author_sort O’Donovan, Daniel J.
collection PubMed
description 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.
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spelling pubmed-32826222012-02-23 A grid-enabled web service for low-resolution crystal structure refinement O’Donovan, Daniel J. Stokes-Rees, Ian Nam, Yunsun Blacklow, Stephen C. Schröder, Gunnar F. Brunger, Axel T. Sliz, Piotr Acta Crystallogr D Biol Crystallogr Research Papers 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. International Union of Crystallography 2012-03-01 2012-02-14 /pmc/articles/PMC3282622/ /pubmed/22349228 http://dx.doi.org/10.1107/S0907444912001163 Text en © O'Donovan et al. 2012 http://creativecommons.org/licenses/by/2.0/uk/ This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
spellingShingle Research Papers
O’Donovan, Daniel J.
Stokes-Rees, Ian
Nam, Yunsun
Blacklow, Stephen C.
Schröder, Gunnar F.
Brunger, Axel T.
Sliz, Piotr
A grid-enabled web service for low-resolution crystal structure refinement
title A grid-enabled web service for low-resolution crystal structure refinement
title_full A grid-enabled web service for low-resolution crystal structure refinement
title_fullStr A grid-enabled web service for low-resolution crystal structure refinement
title_full_unstemmed A grid-enabled web service for low-resolution crystal structure refinement
title_short A grid-enabled web service for low-resolution crystal structure refinement
title_sort grid-enabled web service for low-resolution crystal structure refinement
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3282622/
https://www.ncbi.nlm.nih.gov/pubmed/22349228
http://dx.doi.org/10.1107/S0907444912001163
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