ProFAX: A hardware acceleration of a protein folding algorithm

Protein folding is the physical process by which a sequence of amino acids in a protein folds into its tertiary structure, which determines the functionality of the protein. The knowledge of this structure is crucial for the development of new pharmaceutical therapies. For this reason, many drug industries are interested in applying these kind of algorithms. There are various methods to perform this process, one of the most interesting is Ab Initio modeling. This method creates the 3D-structure from energetic and geometrical features. However, despite its potentiality, companies are slowed down by the high computational needing of the algorithm. A speed-up in the execution time would be crucial to enhance productivity in such industries. In this work we present an accelerated implementation of an Ab Initio Protein Folding Algorithm, based on Monte Carlo simulation. Our implementation is able to reach a speed-up of 1,61x with relation to a pure software implementation, and there is room for more optimization. Furthermore, the algorithm required only 3 weeks to implement, which represents an extremely rapid development time in comparison with typical hardware applications.