High-throughput protein structure determination using grid computing

• Main Authors: Schmidberger, J.W., Bethwaite, B., Enticott, C., Bate, M.A., Androulakis, S.G., Faux, N., Reboul, C.F., Phan, J., Whisstock, J.C., Goscinski, W.J., Garic, S., Abramson, D., Buckle, A.M.
• Format: Conference Proceeding
• Language: English
• Subjects: Biochemistry; Bioinformatics; Biology computing; Crystallization; Crystallography; Genomics; Grid computing; Production; Proteins; X-ray diffraction
• ISSN: 1530-2075
• DOI: 10.1109/IPDPS.2009.5160921

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.