title: Feedback algorithm and web-server for protein structure alignment.
abstract: We have developed a feedback algorithm for protein structure alignment between two protein backbones. A web portal implementing this method has been constructed and is freely available for use at http://fpsa.cs.uno.edu/ with a mirror site at http://fpsa.cs.panam.edu/FPSA/. We compare our algorithm with three other, commonly used methods: CE, DaliLite and SSM. The results show that in most cases our algorithm outputs a larger number of aligned positions when the (Calpha) RMSD is comparable. Also, in many cases where the number of aligned positions is larger or comparable, our learning method is able to achieve a smaller (Calpha) RMSD than the other methods tested. This trend of larger number of aligned positions and smaller (Calpha) RMSD is observed more frequently in cases where the similarity between protein structures is weak.
authors.affiliation: Department of Computer Science, University of New Orleans, New Orleans, LA 70148, USA. zzha2@cs.uno.edu
authors.forename: Zhiyu
authors.initials: Z
authors.lastname: Zhao
authors.forename: Bin
authors.initials: B
authors.lastname: Fu
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Alanis
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Summa
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D020407:Internet; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins