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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2012
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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. |
format | Online Article Text |
id | pubmed-3282622 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
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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