Local Refinement Algorithms for Protein Structure Comparison and Alignment

Abstract

Proteins are an important class of biological macromolecules present in all biological organisms. Protein structures are essential for correct function because it al- lows molecular recognition. Thus protein structures provide the opportunity to recognize homology that is undetectable by sequence comparison, and they are powerful means of discovering functions, yielding direct insight of the molecu- lar mechanisms. In this paper, we propose algorithms and develop tools for local alignment between two protein struc- tures by means of local adjustments.We show the e®ective- ness of the proposed re¯nement methods and initialization algorithms by a set of experiments; the results show im- provement comparing to several previous results.