Open Access

Rigid Molecule Docking: FPGA Reconfiguration for Alternative Force Laws

  • Tom VanCourt1Email author,
  • Yongfeng Gu1,
  • Vikas Mundada1 and
  • Martin Herbordt1
EURASIP Journal on Advances in Signal Processing20062006:097950

https://doi.org/10.1155/ASP/2006/97950

Received: 1 May 2005

Accepted: 1 December 2005

Published: 19 March 2006

Abstract

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 three-dimensional 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 to over a PC.

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Authors’ Affiliations

(1)
Department of Electrical and Computer Engineering, Boston University

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Copyright

© VanCourt et al. 2006