Consensus Based Validation of Membrane Porins

Article type: Research Article

Authors: Katta, A.V.S.K. Mohan | Marikkannu, Rajeshwari | Basaiawmoit, Rajiv V. | Krishnaswamy, Sankaran

Affiliations: Bioinformatics centre, School of Biotechnology, Madurai Kamaraj University, Madurai - 625 021, India. Tel.: +91 452 2459141; Fax: +91 452 2459105

Note: [] Corresponding author. E-mail: [email protected]

Abstract: Porins are outermembrane β-barrel proteins. They have varied biological functionality ranging from phage receptors, immunogenicity, pathogenicity to apoptosis. However, only a small number has been structurally and functionally characterised. A validation mechanism and a database of porins would be useful for target selection in proteomics and structural genomics work. Here we report a validation mechanism developed for membrane porins. A database server for porins, PRNDS, has been created containing experimentally proven porins and likely putative porins. Each porin is validated and ranked using a weighted scoring system developed based on six, structure and sequence based criteria. The server also predicts possible porins.

Keywords: outermembrane, OMP, porin, beta barrel, transmembrane, database server, consensus method, HMM, FastA, Signal peptide, beta strand predicition, pathogenicity

Journal: In Silico Biology, vol. 4, no. 4, pp. 549-561, 2004