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 language | English |
|---|---|
| Title of host publication | IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium |
| DOIs | |
| Publication status | Published - 2009 |
| Event | 23rd IEEE International Parallel and Distributed Processing Symposium, IPDPS 2009 - Rome, Italy Duration: 23 May 2009 → 29 May 2009 |
Conference
| Conference | 23rd IEEE International Parallel and Distributed Processing Symposium, IPDPS 2009 |
|---|---|
| Country | Italy |
| City | Rome |
| Period | 23/05/09 → 29/05/09 |
Cite this
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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 proceeding › Conference Paper › Research › peer-review
TY - GEN
T1 - High-throughput protein structure determination using grid computing
AU - Schmidberger, Jason W.
AU - Bethwaite, Blair
AU - Enticott, Colin
AU - Bate, Mark A.
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.
PY - 2009
Y1 - 2009
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.
UR - http://www.scopus.com/inward/record.url?scp=70449793543&partnerID=8YFLogxK
U2 - 10.1109/IPDPS.2009.5160921
DO - 10.1109/IPDPS.2009.5160921
M3 - Conference Paper
SN - 9781424437504
BT - IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium
ER -