Preliminary Steps Towards Protein Folding Prediction Using Reconfigurable Computing

This paper presents methodologies for the design of a system based on reconfigurable hardware applied to a complex problem in molecular biology: the protein folding problem. Different approaches are explored and advantages and drawbacks are analyzed. Efficient strategies are devised to achieve a significant reduction of the search space of possible foldings. Several simulations are done to evaluate the performance of the system as well as the demand for FPGA´s resources. This work is the base for future hardware implementations aiming at finding the optimal solution for protein folding problems using the 2D-HP model