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Performance analysis and optimization of AMGA for the large-scale virtual screening
Ahn, Sunil,Kim, Namgyu,Lee, Seehoon,Nam, Dukyun,Hwang, Soonwook,Koblitz, Birger,Breton, Vincent,Han, Sangyong John Wiley Sons, Ltd. 2009 SOFTWARE-PRACTICE & EXPERIENCE Vol.39 No.12
<P>This paper addresses performance issues on ARDA Metadata Grid Application (AMGA) and presents new techniques to improve the throughput of AMGA for the WISDOM environment. The first issue is a performance degradation problem when AMGA is used as a metadata service for task retrieval in the WISDOM environment. To deal with the issue, a new AMGA operation designed to reduce the communication overhead required to retrieve a task from AMGA is proposed. According to a performance study conducted with the new operation, the throughput of task retrieval using the proposed operation can be as much as 70 times higher than the throughput when using the existing AMGA operations. The second issue is an AMGA throughput issue in large-scale grid-enabled applications such as WISDOM, where it is not uncommon that thousands of jobs running on grid nodes access the AGMA service simultaneously. To address this issue, integration of a load-balancing technique and a DB connection pool technique into the AMGA are proposed. Test results demonstrate that the performance can be improved linearly in proportion to the number of AMGA servers set up for load balancing; the performance improvement continues until the performance limit of the backend database system is reached. Copyright © 2009 John Wiley & Sons, Ltd.</P>
Design and Discovery of Plasmepsin II Inhibitors Using an Automated Workflow on Large-Scale Grids
Degliesposti, Gianluca,Kasam, Vinod,Da Costa, Ana,Kang, Hee-Kyoung,Kim, Nahyun,Kim, Do-Won,Breton, Vincent,Kim, Doman,Rastelli, Giulio Wiley (John WileySons) 2009 ChemMedChem Vol.4 No.7
<P>Novel and potent inhibitors of Plasmodium falciparum plasmepsin II were identified by post-processing the results of a docking screening with BEAR, a recently reported procedure for the refinement and rescoring of docked ligands in virtual screening. FRET substrate degradation assays performed on the 30 most promising compounds resulted in 26 inhibitors with IC(50) values ranging from 4.3 nM to 1.8 microM.Herein we report the discovery of novel and potent inhibitors of Plasmodium falciparum plasmepsin II using GRID computing infrastructures. These compounds were identified by post-processing the results of a large docking screen of commercially available compounds using an automated procedure based on molecular dynamics refinement and binding free-energy estimation using MM-PBSA and MM-GBSA. Among the best-scored compounds, four highly populated and promising chemical classes were identified: N-alkoxyamidines, guanidines, amides, and ureas and thioureas. Thirty hit compounds representative of each class were selected on the basis of their favourable binding free energies and molecular interactions with key active site residues. These were experimentally validated using an inhibition assay based on FRET substrate degradation. Remarkably, 26 of the 30 tested compounds proved to be active as plasmepsin II inhibitors, with IC(50) values ranging from 4.3 nM to 1.8 microM.</P>