An improved hidden Markov model for transmembrane topology prediction

Proceedings - International Conference on Tools with Artificial Intelligence, ICTAI

Volumn , Issue , 2004, Pages 634-639

  Kahsay, Robel Y ^a   Liao, Li ^b   Gao, Guang ^a  

^a Institute Newark   (United States)

^b University of Delaware   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSOL; HIDDEN MARKOV MODELS (HMM); MEMBRANE PROTEINS; ORGANELLE;

BIOLOGICAL MEMBRANES; CELLS; MATHEMATICAL MODELS; MAXIMUM LIKELIHOOD ESTIMATION; PROTEINS; TOPOLOGY;

MARKOV PROCESSES;

EID: 16244410761     PISSN: 10823409     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICTAI.2004.30     Document Type: Conference Paper

References (12)

1. E. Sonnhammer, G. von Heijne, and A. Krogh, "A hidden Markov model for predicting transmembrane helices in protein sequences", Proceedings of ISMB 6, 1998, pp 175-182.
2. R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, "Biological sequence analysis; probabilistic models of proteins and nucleic acids", Cambridge University Press, 1998.
3. M. Brown, R. Hughey, A. Krogh, I.S. Mian, K. Sjolanderand D. Haussler, "Using Dirichlet Mixture Priors to Derive HiddenMarkov Models for Protein Families", Proc. First International Conference on Intelligent Systems for Molecular Biology, Washington D.C., July, 1993.
4. K. Sjolander, K. Karplus, M. Brown, R. Hughey, A. Krogh, I.S. Mian, D. Haussler, (1996) "Dirichlet Mixtures:A Method for Improved Detection of Weak but Significant Protein Sequence Homology", Comput Appli Biosci 1996, 12, pp. 327-45.
5. A. Krogh, B. Larsson, G. von Heijne, and E. Sonnhammer, "Prediction Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes", Journal of Molecular Biology, 305, pp. 567-580.
6. A. Krogh, M. Brown, I.S. Mian, K. Sjolander, and D. Haussler, "Hidden Markov models in computational biology: Applications to protein modeling", Journal of Molecular Biology, 235, pp. 1501-1531.
7. B. Persson, and P. Argos, "Prediction of transmembrane protein topology utilizing multiple sequence alignments", Journal of Protein Chem., 16, pp. 453-457.
8. B. Rost, P. Fariselli, and R. Casadio, "Topology prediction for helical transmembrane proteins at 86% accuracy", Protein Sci., 5, 1996, pp. 1704-1718.
9. G. von Heijne, "The distribution of positively charged residues in bacterial inner membrane proteins correlates with the transmembrane topology", EMBO Journal, 5, pp. 3021-3027.
10. G. von Heijne, "Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule." Journal of Molecular Biology, 225, pp. 487-494.
11. G. von Heijne, "Membrane proteins: from sequence to structure", Annu. Rev. Biophys. Biomol. Struct., 23, pp. 167-192.
12. C. Branden and J. Tooze, Introduction to structure, Garland Publishing Inc., U.S.A. 1998