Exploring protein fold space by secondary structure prediction using data distribution method on Grid platform.
BACKGROUND
Since the newly developed Grid platform has been considered as a powerful tool to share resources in the Internet environment, it is of interest to demonstrate an efficient methodology to process massive biological data on the Grid environments at a low cost. This paper presents an efficient and economical method based on a Grid platform to predict secondary structures of all proteins in a given organism, which normally requires a long computation time through sequential execution, by means of processing a large amount of protein sequence data simultaneously. From the prediction results, a genome scale protein fold space can be pursued.


RESULTS
Using the improved Grid platform, the secondary structure prediction on genomic scale and protein topology derived from the new scoring scheme for four different model proteomes was presented. This protein fold space was compared with structures from the Protein Data Bank, database and it showed similarly aligned distribution. Therefore, the fold space approach based on this new scoring scheme could be a guideline for predicting a folding family in a given organism.
Lee
Soojin
S
Distributed and Mobile Computing Laboratory, Graduate School of Information and Communication, Ajou University, Suwon 442-749, Korea.
Cho
Min-Kyu
MK
Jung
Jin-Won
JW
Kim
Jai-Hoon
JH
Lee
Weontae
W
D003205:Computing Methodologies; D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods*; D008956:Models, Chemical; D017433:Protein Structure, Secondary; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
D011506:Proteins