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.