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 Citations (Scopus)

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 2012

Fingerprint

Running
X-Rays
Datasets

Keywords

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

ASJC Scopus subject areas

  • Structural Biology

Cite this

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

A grid-enabled web service for low-resolution crystal structure refinement. / Odonovan, Daniel J.; Stokes-Rees, Ian; Nam, Yunsun; Blacklow, Stephen C.; Schröder, Gunnar F.; Brunger, Axel T.; Sliz, Piotr.

In: Acta Crystallographica Section D: Biological Crystallography, Vol. 68, No. 3, 03.2012, p. 261-267.

Research output: Contribution to journalArticle

Odonovan, DJ, Stokes-Rees, I, Nam, Y, Blacklow, SC, Schröder, GF, Brunger, AT & Sliz, P 2012, 'A grid-enabled web service for low-resolution crystal structure refinement', Acta Crystallographica Section D: Biological Crystallography, vol. 68, no. 3, pp. 261-267. https://doi.org/10.1107/S0907444912001163
Odonovan, 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. In: Acta Crystallographica Section D: Biological Crystallography. 2012 ; Vol. 68, No. 3. pp. 261-267.
@article{218939b045a3401280ada7dc0efcc4e4,
title = "A grid-enabled web service for low-resolution crystal structure refinement",
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.",
keywords = "deformable elastic network restraints, DEN refinement, low-resolution refinement",
author = "Odonovan, {Daniel J.} and Ian Stokes-Rees and Yunsun Nam and Blacklow, {Stephen C.} and Schr{\"o}der, {Gunnar F.} and Brunger, {Axel T.} and Piotr Sliz",
year = "2012",
month = "3",
doi = "10.1107/S0907444912001163",
language = "English (US)",
volume = "68",
pages = "261--267",
journal = "Acta Crystallographica Section D: Structural Biology",
issn = "0907-4449",
publisher = "John Wiley and Sons Inc.",
number = "3",

}

TY - JOUR

T1 - A grid-enabled web service for low-resolution crystal structure refinement

AU - Odonovan, Daniel J.

AU - Stokes-Rees, Ian

AU - Nam, Yunsun

AU - Blacklow, Stephen C.

AU - Schröder, Gunnar F.

AU - Brunger, Axel T.

AU - Sliz, Piotr

PY - 2012/3

Y1 - 2012/3

N2 - 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.

AB - 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.

KW - deformable elastic network restraints

KW - DEN refinement

KW - low-resolution refinement

UR - http://www.scopus.com/inward/record.url?scp=84856697357&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84856697357&partnerID=8YFLogxK

U2 - 10.1107/S0907444912001163

DO - 10.1107/S0907444912001163

M3 - Article

C2 - 22349228

AN - SCOPUS:84856697357

VL - 68

SP - 261

EP - 267

JO - Acta Crystallographica Section D: Structural Biology

JF - Acta Crystallographica Section D: Structural Biology

SN - 0907-4449

IS - 3

ER -