(Received: July 12, 2005; Accepted for publication: November 9, 2005; Published on Web: December 15, 2005)
We developed an integrated environment for virtual screening, Xsi, based on the force field method. Two methodologies, Ligand Based Drug Design(LBDD) and Structure Based Drug Design(SBDD) are both implemented on the same platform and users can realize various analysis flows by specially designed Xsi-Script.
Calculation for conformation search on small molecules is parallelized on EHPC-SH4, with an efficiency of 96.6% by 21 CPUs.
As a test calculation for SBDD, re-docking was performed for a complex of c-ABL, and sufficiently small RMSD(0.13A) was obtained.
Keywords: Force field method, Special purpose computer, Ligand based drug design, Structure based drug design
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