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iPBA: a tool for protein structure comparison using sequence alignment strategies
- Gelly, Jean-Christophe, Joseph, Agnel Praveen, Srinivasan, Narayanaswamy, de Brevern, Alexandre G.
- Nucleic acids research 2011 v.39 no.suppl_2 pp. W18
- Internet, databases, nucleic acids, protein structure, sequence alignment
- 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/.