Acceleration of a protein structure comparison algorithm on FPGA

摘要

Proteins are among the most fundamental molecules in living organisms. Investigation and comparison of their three-dimensional structure is an important task in structural bioinformatics as global and local similarities can be of functional importance. Structure alignment and comparison is computationally intensive, so typically a number of simplifications are used for practical reasons. However, these can not always be justified on a biological or biochemical basis, and might lead to unreliable results. In this paper we describe the development and application of a method based on local structural information, suitable for comprehensive analysis of the more than 100,000 structures available today. The approach is implemented on an FPGA board allowing reasonable runtime and thus offering the possibility of parameter tuning on very large, unbiased datasets.