Efficiency Enhancement of Protein Folding for Complete Molecular Simulation via Hardware Computing

Accelerating a protein folding by implementing it in a reconfigurable field programmable gate array (FPGA) is described. 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. This paper employed VMD tool and force field simulation theorem based on FPGA for protein folding solution. This technique consists of two components: finished protein folding process and found out active sites for drug docking. The goal of protein folding simulation is to search the global energy minimum location with stability state and the when the protein is finished the folding task, we can find out the active sites for pre-process of ligand protein docking. 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 FPGApsilas resources.