Scoring hidden Markov models to discriminate β-barrel membrane proteins

Computational Biology and Chemistry

Volumn 28, Issue 3, 2004, Pages 189-194

  Deng, Yong ^a   Liu, Qi ^b   Li, Yi Xue ^b  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

Barrel membrane proteins; Hidden Markov model; Log odds score

Indexed keywords

GENES; HYDROPHILICITY; HYDROPHOBICITY; INTERFACES (MATERIALS); MARKOV PROCESSES; MEMBRANES;

Β-BARREL MEMEBRANE PROTEINS; HIDDEN MARKOV MODEL; LOG-ODDS SCORE; NULL MODELS;

PROTEINS;

MEMBRANE PROTEIN; PROTEOME;

ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; COMPARATIVE STUDY; GENETICS; METHODOLOGY; PROBABILITY; PROTEIN DATABASE; PROTEIN MOTIF; PSEUDOMONAS AERUGINOSA; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STRUCTURAL HOMOLOGY;

ALGORITHMS; AMINO ACID MOTIFS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MARKOV CHAINS; MEMBRANE PROTEINS; PROTEOME; PSEUDOMONAS AERUGINOSA; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 3142529119     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2004.02.004     Document Type: Article

References (15)

1. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28:2000;235-242.
2. Bowie J.U. Are we destined to repeat history. Curr. Opin. Struct. Biol. 10:2000;435-437.
3. Diederichs K., Freigang J., Umhau S., Zeth K., Breed J. Prediction by a neural network of outer membrane beta-strand protein topology. Protein Sci. 7:1998;2413-2420.
4. Drummelsmith J., Whitfield C. Translocation of group 1 capsular polysaccharide to the surface of Escherichia coli requires a multimeric complex in the outer membrane. EMBO J. 19:2000;57-66.
5. Jacoboni I., Martelli P.L., Fariselli P., De Pinto V., Casadio R. Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor. Protein Sci. 10:2001;779-787.
6. Liu Q., Zhu Y.S., Wang B.H., Li Y.X. A HMM-based method to predict the transmembrane regions of beta-barrel membrane proteins. Comput. Biol. Chem. 27:2003;69-76.
7. Martelli P.L., Fariselli P., Krogh A., Casadio R. A sequence-profile- based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics. 18(Suppl. 1):2002;S46-S53.
8. Pohlmeyer K., Soll J., Steinkamp T., Hinnah S.C., Wagner R. Isolation and characterization of an amino acid-selective channel protein present in the chloroplastic outer envelope membrane. Proc. Natl. Acad. Sci. U.S.A. 94:1997;9504-9509.
9. Rabiner L.R. A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE. 77:1989;257-286.
10. Saier M.H. Jr. A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol. Mol. Biol. Rev. 64:2000;354-411.
11. Schulz G.E. beta-Barrel membrane proteins. Curr. Opin. Struct. Biol. 10:2000;443-447.
12. Steinkamp T., Hill K., Hinnah S.C., Wagner R., Rohl T., Pohlmeyer K., Soll J. Identification of the pore-forming region of the outer chloroplast envelope protein OEP16. J. Biol. Chem. 275:2000;11758-11764.
13. Wimley W.C. Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures. Protein Sci. 11:2002;301-312.
14. Yen M.R., Peabody C.R., Partovi S.M., Zhai Y., Tseng Y.H., Saier M.H. Protein-translocating outer membrane porins of Gram-negative bacteria. Biochim. Biophys. Acta. 1562:2002;6-31.
15. Zhai Y., Saier M.H. Jr. The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes. Protein Sci. 11:2002;2196-2207.