High-throughput protein structure determination using grid computing

Jason W. Schmidberger, Blair Bethwaite, Colin Enticott, Mark A. Bate, Steve G. Androulakis, Noel Faux, Cyril F. Reboul, Jennifer M N Phan, James C. Whisstock, Wojtek J. Goscinski, Slavisa Garic, David Abramson, Ashley M. Buckle

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

2 Citations (Scopus)

Abstract

Determining the X-ray crystallographic structures of proteins using the technique of molecular replacement (MR) can be a time and labor-intensive trial-and-error process, involving evaluating tens to hundreds of possible solutions to this complex 3D jigsaw puzzle. For challenging cases indicators of success often do not appear until the later stages of structure refinement, meaning that weeks or even months could be wasted evaluating MR solutions that resist refinement and do not lead to a final structure. In order to improve the chances of success as well as decrease this timeframe, we have developed a novel grid computing approach that performs many MR calculations in parallel, speeding up the process of structure determination from weeks to hours. This high-throughput approach also allows parameter sweeps to be performed in parallel, improving the chances of MR success.

Original languageEnglish
Title of host publicationIPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium
DOIs
Publication statusPublished - 2009
EventIEEE International Parallel and Distributed Processing Symposium, 2009 - Rome, Italy
Duration: 23 May 200929 May 2009
Conference number: 23rd

Conference

ConferenceIEEE International Parallel and Distributed Processing Symposium, 2009
Abbreviated titleIPDPS 2009
CountryItaly
CityRome
Period23/05/0929/05/09

Cite this

Schmidberger, J. W., Bethwaite, B., Enticott, C., Bate, M. A., Androulakis, S. G., Faux, N., ... Buckle, A. M. (2009). High-throughput protein structure determination using grid computing. In IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium [5160921] https://doi.org/10.1109/IPDPS.2009.5160921