title: MatAlign: precise protein structure comparison by matrix alignment.
abstract: We propose a detailed protein structure alignment method named "MatAlign". It is a two-step algorithm. Firstly, we represent 3D protein structures as 2D distance matrices, and align these matrices by means of dynamic programming in order to find the initially aligned residue pairs. Secondly, we refine the initial alignment iteratively into the optimal one according to an objective scoring function. We compare our method against DALI and CE, which are among the most accurate and the most widely used of the existing structural comparison tools. On the benchmark set of 68 protein structure pairs by Fischer et al., MatAlign provides better alignment results, according to four different criteria, than both DALI and CE in a majority of cases. MatAlign also performs as well in structural database search as DALI does, and much better than CE does. MatAlign is about two to three times faster than DALI, and has about the same speed as CE. The software and the supplementary information for this paper are available at http://xena1.ddns.comp.nus.edu.sg/~genesis/MatAlign/.
authors.affiliation: Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore. azeyar@i2r.a-star.edu.sg
authors.forename: Zeyar
authors.initials: Z
authors.lastname: Aung
authors.forename: Kian-Lee
authors.initials: KL
authors.lastname: Tan
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009716:Numerical Analysis, Computer-Assisted; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins