Hardware Acceleration of STON Algorithm for Comparing 3-D Structure of Proteins

Comparing three-dimensional structure of proteins is one of the most fundamental problems in bioinformatics. In recent years, various algorithms have been proposed to solve this problem efficiently. The proposed algorithms are very time-consuming due to high complexity and large input data. In this paper, hardware acceleration is applied to minimize the execution time of a previous algorithm, called STON. An FPGA-based hardware is presented to perform this task in a fast manner. An average speed-up of 2.5x is achieved compared to the software execution.