Consensus based validation of membrane porins

In Silico Biology

Volumn 4, Issue 4, 2004, Pages 549-561

  Mohan Katta, A V S K ^a   Marikkannu, Rajeshwari ^a   Basaiawmoit, Rajiv V ^a   Krishnaswamy, Sankaran ^a  

^a MADURAI KAMARAJ UNIVERSITY   (India)

Author keywords

Beta barrel; Beta strand predicition; Consensus method; Database server; FastA; HMM; OMP; Outermembrane; Pathogenicity; Porin; Signal peptide; Transmembrane

Indexed keywords

PORIN; RNA;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CONSENSUS; CONTROLLED STUDY; GENETIC ALGORITHM; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PROTEIN DATABASE; PROTEIN STRUCTURE; SCORING SYSTEM; VALIDATION PROCESS;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; CONSENSUS SEQUENCE; DATABASES, PROTEIN; GENOMICS; PORINS; PROTEOMICS;

EID: 14944343471     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (19)

1. Arockiasamy, A. and Krishnaswamy, S. (2000). Homology model of surface antigen ompc from Salmonella typhi and its functional implications. J. Biomol. Struct. Dyn. 18, 261-271.
2. Bagos, P. G., Liakopoulos, T. D., Spyropoulos, I. C. and Hamodrakas, S. J. (2004). A Hidden Markov Model method, capable of predicting and discriminating β-barrel outer membrane proteins. BMC Bioinformatics 5, 29.
3. Casadio, R., Fariselli, P., Finocchiaro, G. and Martelli, P. L. (2003). Fishing new proteins in the twilight zone of genomes: The test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria. Protein Sci. 12 1158-1168.
4. Chen, C. P. and Rost, B. (2002). State of the art in membrane protein prediction. Appl. Bioinformatics 1, 21-35.
5. Gnanasekaran, T. V., Peri, S., Arockiasamy, A. and Krishnaswamy, S. (2000). Profiles from structure based sequence alignment of porins can identify β stranded integral membrane proteins. Bioinformatics 16 839-842.
6. Gromiha, M. M., Majumdar, R. and Ponnuswamy, P. K. (1997). Identification of membrane spanning beta strands in bacterial porins. Protein Eng. 10, 497-500.
7. Ho, T. D. and Slauch, J. M. (2001). Ompc is the receptor for gifsy-1 and gifsy-2 bacteriophages of Salmonella. J. Bacteriol. 183, 1495-1498.
8. Jacoboni, I., Martelli, P. L., Fariselli, P., De Pinto, V. and Casadio, R. (2001). Prediction of the transmembrane regions of β-barrel membrane proteins with a neural network-based predictor. Protein Sci. 10, 779-787.
9. Merino, S., Nogueras, M. M., Aguilar, A., Rubires, X., Albertí, S., Benedí, V. J. and Tomás, J. M. (1998). Activation of the complement classical pathway (C1q binding) by mesophilic Aeromonas hydrophila outer membrane protein. Infect. Immun. 66, 3825-3831.
10. Müller, A., Rassow, J., Grimm, J., Machuy, N., Meyer, T. F. and Rudel, T. (2002). Vdac and the bacterial porin porb of Neisseria gonorrhoeae share mitochondrial import pathways. EMBO. J. 21, 1916-1929.
11. Murzin, A. G., Brenner, S. E., Hubbard, T. and Chothia, C. (1995). SCOP: a structural classification of protein database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
12. Rodrigues, A. and Hubbard, R. E. (2003). Making decisions for structural genomics. Brief. Bioinform. 4, 150-167.
13. Saier, M. H. jr. (2000a). Families of proteins forming transmembrane channels. J. Membr. Biol. 175, 165-180.
14. Saier, M. H. jr. (2000b). A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol. Mol. Biol. Rev. 64, 354-411.
15. Schirmer, T. and Cowan, S. W. (1993). Prediction of membrane spanning beta-strands and its application to maltoporin. Protein Sci. 2, 1361-1363.
16. Schulz, G. E. (1996). Porins: General to specific, native to engineered passive pores. Curr. Opin. Struct. Biol. 6, 485-490.
17. Singh, M., Vohra, H., Kumar, L. and Ganguly, N. K. (1999). Induction of systemic and mucosal immune response in mice immunised with porins of Salmonella Typhi. J. Med. Microbiol. 48, 79-88.
18. Wimley, W. (2002). Toward genomic identification of β-barrel membrane proteins: Composition and architecture of known structures. Protein Sci. 11, 301-312.
19. Zhai, Y. and Saier, M. H. jr. (2002). The β-barrel finder (bbf) program, allowing identification of outermembrane β-barrel proteins encoded within prokaryotic genomes. Protein Sci. 11, 2196-2207.