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

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
Event23rd IEEE International Parallel and Distributed Processing Symposium, IPDPS 2009 - Rome, Italy
Duration: 23 May 200929 May 2009

Conference

Conference23rd IEEE International Parallel and Distributed Processing Symposium, IPDPS 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
Schmidberger, Jason W. ; Bethwaite, Blair ; Enticott, Colin ; Bate, Mark A. ; Androulakis, Steve G. ; Faux, Noel ; Reboul, Cyril F. ; Phan, Jennifer M N ; Whisstock, James C. ; Goscinski, Wojtek J. ; Garic, Slavisa ; Abramson, David ; Buckle, Ashley M. / High-throughput protein structure determination using grid computing. IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium. 2009.
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title = "High-throughput protein structure determination using grid computing",
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.",
author = "Schmidberger, {Jason W.} and Blair Bethwaite and Colin Enticott and Bate, {Mark A.} and Androulakis, {Steve G.} and Noel Faux and Reboul, {Cyril F.} and Phan, {Jennifer M N} and Whisstock, {James C.} and Goscinski, {Wojtek J.} and Slavisa Garic and David Abramson and Buckle, {Ashley M.}",
year = "2009",
doi = "10.1109/IPDPS.2009.5160921",
language = "English",
isbn = "9781424437504",
booktitle = "IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium",

}

Schmidberger, JW, Bethwaite, B, Enticott, C, Bate, MA, Androulakis, SG, Faux, N, Reboul, CF, Phan, JMN, Whisstock, JC, Goscinski, WJ, Garic, S, Abramson, D & Buckle, AM 2009, High-throughput protein structure determination using grid computing. in IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium., 5160921, 23rd IEEE International Parallel and Distributed Processing Symposium, IPDPS 2009, Rome, Italy, 23/05/09. https://doi.org/10.1109/IPDPS.2009.5160921

High-throughput protein structure determination using grid computing. / Schmidberger, Jason W.; Bethwaite, Blair; Enticott, Colin; Bate, Mark A.; Androulakis, Steve G.; Faux, Noel; Reboul, Cyril F.; Phan, Jennifer M N; Whisstock, James C.; Goscinski, Wojtek J.; Garic, Slavisa; Abramson, David; Buckle, Ashley M.

IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium. 2009. 5160921.

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

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AU - Androulakis, Steve G.

AU - Faux, Noel

AU - Reboul, Cyril F.

AU - Phan, Jennifer M N

AU - Whisstock, James C.

AU - Goscinski, Wojtek J.

AU - Garic, Slavisa

AU - Abramson, David

AU - Buckle, Ashley M.

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N2 - 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.

AB - 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.

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Schmidberger JW, Bethwaite B, Enticott C, Bate MA, Androulakis SG, Faux N et al. High-throughput protein structure determination using grid computing. In IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium. 2009. 5160921 https://doi.org/10.1109/IPDPS.2009.5160921