title: iPBA: a tool for protein structure comparison using sequence alignment strategies.
abstract: With the immense growth in the number of available protein structures, fast and accurate structure comparison has been essential. We propose an efficient method for structure comparison, based on a structural alphabet. Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide conformations that can fairly approximate a complete protein chain. Thus a 3D structure can be translated into a 1D sequence of PBs. With a simple Needleman-Wunsch approach and a raw PB substitution matrix, PB-based structural alignments were better than many popular methods. iPBA web server presents an improved alignment approach using (i) specialized PB Substitution Matrices (SM) and (ii) anchor-based alignment methodology. With these developments, the quality of ∼88% of alignments was improved. iPBA alignments were also better than DALI, MUSTANG and GANGSTA(+) in >80% of the cases. The webserver is designed to for both pairwise comparisons and database searches. Outputs are given as sequence alignment and superposed 3D structures displayed using PyMol and Jmol. A local alignment option for detecting subs-structural similarity is also embedded. As a fast and efficient 'sequence-based' structure comparison tool, we believe that it will be quite useful to the scientific community. iPBA can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/ipba/.
authors.affiliation: INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, Université Paris Diderot-Paris 7, Institut National de la Transfusion Sanguine, 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France.
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Gelly
authors.forename: Agnel Praveen
authors.initials: AP
authors.lastname: Joseph
authors.forename: Narayanaswamy
authors.initials: N
authors.lastname: Srinivasan
authors.forename: Alexandre G
authors.initials: AG
authors.lastname: de Brevern
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D011487:Protein Conformation; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D012984:Software