STON: A novel method for protein three-dimensional structure comparison

Protein structure comparison is an important problem in bioinformatics and has many applications in the study of structural and functional genomics. During the last decades, various heuristic methods have been developed to solve the protein structure comparison problem. Most of the protein structure comparison methods give the alignment based on the minimum RMSD (root mean square deviation) and ignore many significant local alignments that may be important for evolutional or functional studies. We have developed a new algorithm to find aligned residues in two proteins with desired RMSD value. The parameterized distance and rotation in this program enable us to search for strongly or weakly similar aligned fragments in two proteins.