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

Acta Crystallographica. Section D, Biological Crystallography
Daniel J O'DonovanPiotr Sliz

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.

References

Oct 3, 1998·Acta Crystallographica. Section D, Biological Crystallography·A T BrüngerG L Warren
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Mar 15, 2006·Cell·Jeffrey J Wilson, Rhett A Kovall
Aug 11, 2007·Science·Isaiah T ArkinDavid E Shaw
Apr 3, 2008·The Journal of Biological Chemistry·David R FriedmannRhett A Kovall
Jan 28, 2009·Acta Crystallographica. Section D, Biological Crystallography·Axel T BrungerWilliam I Weis
Apr 9, 2010·Nature·Gunnar F SchröderAxel T Brunger
Nov 26, 2010·Proceedings of the National Academy of Sciences of the United States of America·Ian Stokes-Rees, Piotr Sliz
Feb 14, 2012·Structure·Sung Hee ChoiStephen C Blacklow

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Citations

Apr 13, 2013·Nature·Sebastian GeibelGabriel Waksman
Nov 13, 2013·Proceedings of the National Academy of Sciences of the United States of America·Brian BaeSeth A Darst
Sep 17, 2013·ELife·Andrew MorinPiotr Sliz
Jul 22, 2015·Proceedings of the National Academy of Sciences of the United States of America·Brian BaeSeth A Darst
Mar 1, 2016·Cell Reports·Kyle W MuirDaniel Panne
Feb 14, 2012·Structure·Sung Hee ChoiStephen C Blacklow
Nov 4, 2015·Acta Crystallographica. Section D, Biological Crystallography·Chong ZhangJianpeng Ma
May 27, 2016·The EMBO Journal·Carmen Aguilar-GurrieriDaniel Panne
Jul 6, 2013·Biopolymers·Andrew Morin, Piotr Sliz

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Software Mentioned

Django
GlideinWMS
MySQL
CNS
DEN
refinement
SBGrid
Apache
Virtual Data Toolkit
Enthought Python

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