Reconfigurable computing for accelerating protein folding simulations

Authors:
Nilton B. Armstrong, Jr.;Heitor S. Lopes;Carlos R. Erig Lima
Affiliations:
Bioinformatics Laboratory, Federal University of Technology - Paraná, Curitiba, PR, Brazil and Technology Institute of Paraná, Curitiba, PR, Brazil;Bioinformatics Laboratory, Federal University of Technology - Paraná, Curitiba, PR, Brazil;Bioinformatics Laboratory, Federal University of Technology - Paraná, Curitiba, PR, Brazil
Venue:
ARC'07 Proceedings of the 3rd international conference on Reconfigurable computing: architectures, tools and applications
Year:
2007

Citing 2
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Abstract

This paper presents a methodology for the design of a reconfigurable computing system applied to a complex problem in molecular Biology: the protein folding problem. An efficient hardware-based approach was devised to achieve a significant reduction of the search space of possible foldings. Several simulations were done to evaluate the performance of the system as well as the demand for FPGA's resources. Also a complete desktop-FPGA system was developed. This work is the base for future hardware implementations aimed at finding the optimal solution for protein folding problems using the 2D-HP model.