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

Daniel J. Odonovan, Ian Stokes-Rees, Yunsun Nam, Stephen C. Blacklow, Gunnar F. Schröder, Axel T. Brunger, Piotr Sliz

Research output: Contribution to journalArticle

14 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)261-267
Number of pages7
JournalActa Crystallographica Section D: Biological Crystallography
Volume68
Issue number3
DOIs
StatePublished - Mar 1 2012

Keywords

  • DEN refinement
  • deformable elastic network restraints
  • low-resolution refinement

ASJC Scopus subject areas

  • Structural Biology

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    Odonovan, D. J., Stokes-Rees, I., Nam, Y., Blacklow, S. C., Schröder, G. F., Brunger, A. T., & Sliz, P. (2012). A grid-enabled web service for low-resolution crystal structure refinement. Acta Crystallographica Section D: Biological Crystallography, 68(3), 261-267. https://doi.org/10.1107/S0907444912001163