title: Iterative non-sequential protein structural alignment.
abstract: Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at http://www.cs.rpi.edu/~zaki/software/SNAP.
authors.affiliation: Department of Computer Science, Rensselaer Polytechnic Institute, 110 8th st. Troy, New York 12180, USA. salems@cs.rpi.edu
authors.forename: Saeed
authors.initials: S
authors.lastname: Salem
authors.forename: Mohammed J
authors.initials: MJ
authors.lastname: Zaki
authors.forename: Christopher
authors.initials: C
authors.lastname: Bystroff
mesh_terms: D019747:Aldose-Ketose Isomerases / Q000737:chemistry; D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry; D016000:Cluster Analysis; D019295:Computational Biology; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry; D030562:Databases, Protein; D007874:Leghemoglobin / Q000737:chemistry; D008958:Models, Molecular; D009251:NADPH-Ferrihemoprotein Reductase / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012372:ROC Curve; D012984:Software; D040681:Structural Homology, Protein; D013836:Thiamin Pyrophosphokinase / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D007874:Leghemoglobin; D011506:Proteins; D003577:Cytochrome P-450 Enzyme System; D009251:NADPH-Ferrihemoprotein Reductase; C052423:flavocytochrome P450 BM3 monoxygenases; D013836:Thiamin Pyrophosphokinase; C020582:glucosamine-6-phosphate isomerase; D019747:Aldose-Ketose Isomerases