Tuyển tập báo cáo các nghiên cứu khoa học quốc tế ngành hóa học dành cho các bạn yêu hóa học tham khảo đề tài: Rigid Molecule Docking: FPGA Reconfiguration for Alternative Force Laws | Hindawi Publishing Corporation EURASIP Journal on Applied Signal Processing Volume 2006 Article ID 97950 Pages 1-10 DOI ASP 2006 97950 Rigid Molecule Docking FPGA Reconfiguration for Alternative Force Laws Tom VanCourt Yongfeng Gu Vikas Mundada and Martin Herbordt Department of Electrical and Computer Engineering Boston University Boston MA 02215 USA Received 1 May 2005 Revised 7 September 2005 Accepted 1 December 2005 Molecular docking is one of the primary computational methods used by pharmaceutical companies to try to reduce the cost of drug discovery. A common docking technique used for low-resolution screening or as an intermediate step performs a threedimensional correlation between two molecules to test for favorable interactions between them. We extend our previous work on FPGA-based docking accelerators using reconfigurability for customization of the physical laws and geometric models that describe molecule interaction. Our approach based on direct summation allows straightforward combination of multiple forces and enables nonlinear force models the latter in particular are incompatible with the transform-based techniques typically used. Our approach has the further advantage of supporting spatially oriented values in molecule models as well as the detection of multiple positions representing favorable interactions. We report performance measurements on several different models of chemical behavior and show speedups of from 130 X to 1100 X over a PC. Copyright 2006 Hindawi Publishing Corporation. All rights reserved. 1. INTRODUCTION Noncovalent bonding between molecules is basic to the processes of life and to the effectiveness of pharmaceuticals. Chemical experiments are not always practical for measuring binding strength and may be prohibitively expensive for screening 100 000 or more drug candidates against one molecule of medical importance. Instead a number of computational approaches have been developed. The most precise computational .
