TY - GEN
T1 - Implementation of protein tertiary structure prediction system with NetSolve
AU - Tanimura, Yusuke
AU - Aoi, Keiko
AU - Hiroyasu, Tomoyuki
AU - Miki, Mitsunori
AU - Okamoto, Yuko
AU - Dongarra, Jack
PY - 2004
Y1 - 2004
N2 - In this study, the protein tertiary structure prediction systems on the Grid are proposed for progress of the bioinformatics. The prediction is mainly performed by the protein energy minimization. However, this method has many iterated calculation of the protein energy in most cases. To use the Grid as the large-scale computing environment would be valuable for this system. In the system, Parallel Simulated Annealing using Genetic Crossover (PSA/GAc) is a minimization engine and NetSolve is a basic tool to use the Grid. In this study, two types of implementations are prepared. The first naive implementation of the system has a critical overhead due to large communication delay over the Internet. The second system, asynchronous Crossover model, improves the performance in the second implementation. The details of the system and the experimental results solving C-peptide are shown as an example of Grid application.
AB - In this study, the protein tertiary structure prediction systems on the Grid are proposed for progress of the bioinformatics. The prediction is mainly performed by the protein energy minimization. However, this method has many iterated calculation of the protein energy in most cases. To use the Grid as the large-scale computing environment would be valuable for this system. In the system, Parallel Simulated Annealing using Genetic Crossover (PSA/GAc) is a minimization engine and NetSolve is a basic tool to use the Grid. In this study, two types of implementations are prepared. The first naive implementation of the system has a critical overhead due to large communication delay over the Internet. The second system, asynchronous Crossover model, improves the performance in the second implementation. The details of the system and the experimental results solving C-peptide are shown as an example of Grid application.
UR - http://www.scopus.com/inward/record.url?scp=11244334223&partnerID=8YFLogxK
U2 - 10.1109/HPCASIA.2004.1324052
DO - 10.1109/HPCASIA.2004.1324052
M3 - Conference contribution
AN - SCOPUS:11244334223
SN - 076952138X
SN - 9780769521381
T3 - Proceedings - Seventh International Conference on High Performance Computing and Grid in Asia Pacific Region, HPCAsia 2004
SP - 320
EP - 327
BT - Proceedings - Seventh International Conference on High Performance Computing and Grid in Asia Pacific Region, HPCAsia 2004
T2 - Proceedings - Seventh International Conference on High Performance Computing and Grid in Asia Pacific Region, HPCAsia 2004
Y2 - 20 July 2004 through 22 July 2004
ER -