Reconfigurable Computing for Accelerating Protein Folding Simulations

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.

• Type: Conference
• Year: 2007
• Where: ARC
• Authors: Nilton B. Armstrong, Heitor S. Lopes, Carlos R. Erig Lima
• Keywords: ARC 2007, Efficient Hardware-based Approach, Future Hardware Implementations, Hardware, Protein Folding Problems