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.
This work was partially supported by the Brazilian National Research Council – CNPq, under research grants no. 305720/2004-0 and 506479/2004-8.
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Armstrong, N.B., Lopes, H.S., Lima, C.R.E. (2007). Reconfigurable Computing for Accelerating Protein Folding Simulations. In: Diniz, P.C., Marques, E., Bertels, K., Fernandes, M.M., Cardoso, J.M.P. (eds) Reconfigurable Computing: Architectures, Tools and Applications. ARC 2007. Lecture Notes in Computer Science, vol 4419. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71431-6_29
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DOI: https://doi.org/10.1007/978-3-540-71431-6_29
Publisher Name: Springer, Berlin, Heidelberg
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