Predicting protein structure using hidden Markov models

Proteins: Structure, Function and Genetics

Volumn 29, Issue SUPPL. 1, 1997, Pages 134-139

  Karplus, Kevin ^a   Sjölander, Kimmen ^a   Barrett, Christian ^a   Cline, Melissa ^a   Haussler, David ^a   Hughey, Richard ^a   Holm, Liisa ^b   Sander, Chris ^b  

^a University of California Santa Cruz   (United States)

^b NONE

Author keywords

CASP2; Fold recognition; HMM; Remote homology; Structure library

Indexed keywords

ARTICLE; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; PROBABILITY; REPRODUCIBILITY; SEQUENCE ALIGNMENT;

PROTEIN;

MARKOV CHAINS; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT;

EID: 0031301752     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(1997)1+<134::AID-PROT18>3.0.CO;2-P     Document Type: Article

References (24)

1. Altschul, S.F. Amino acid substitution matrices from an information theoretic perspective. JMB 219:555-565, 1991.
2. Barrett, C., Hughey, R., Karplus, K. Scoring hidden Markov models. CABIOS 13:191-199, 1997.
3. Berger, J. "Statistical Decision Theory and Bayesian Analysis." Springer-Verlag, New York, 1985.
4. Bernardo, J., Smith, A. "Bayesian Theory." John Wiley & Sons, Inc., New York, 1994.
5. Doolittle, R.F. "Of URFs and ORFs: A Primer on How to Analyze Derived Amino Acid Sequences." University Science Books, Mill Valley, California, 1986.
6. Eddy, S. Hidden Markov models. Curr. Opin. Struct. Biol. 6:361-365, 1996.
7. Fischer, D., Eisenberg, D. Protein fold recognition using sequence-derived predictions. Protein Sci. 5:947-955, 1996.
8. Henikoff, S., Henikoff, J.G. Position-based sequence weights. JMB 243:574-578, 1994.
9. Holm, L., Sander, C. Evaluation of protein models by atomic solvation preference. JMB 225:93-105, 1992.
10. Holm, L., Sander, C. Fast and simple monte-carlo algorithm for side chain optimization in proteins: Application to model building by homology. Proteins 14:213-223, 1992.
11. Holm, L., Sander, C. Protein structure comparison by alignment of distance matrices. JMB 233:123-138, 1993.
12. Hughey, R., Krogh, A. Hidden Markov models for sequence analysis: Extension and analysis of the basic method. CABIOS 12:95-107, 1996.
13. Jones, D., Thornton, J. Protein fold recognition. J. Comput. Aided Mol. Des. 7:439-456, 1993.
14. Karplus, K., Sjölander, Kimmen, Barrett, C., Cline, M., Haussler, D., Hughey, R., Holm, L., Sander, C. Predicting protein structure using hidden Markov models, the CASP2 contest. Technical Report UCSC-CRL-97-13, University of California, Santa Cruz, Computer Science, UC Santa Cruz, CA 95064, 1997.
15. Krogh, A., Brown, M., Mian, I.S., Sjölander, K., Haussler, D. Hidden Markov models in computational biology: Applications to protein modeling. JMB 235:1501-1531, 1994.
16. Lathrop, R., Ljubomir, L., Nambudripad, R., White, J., Conte, L.L., Bryant, B., Smith, T. Threading through the levinthal paradox. Nature, in press.
17. Lemer, C., Rooman, M., Wodak, S. Protein structure prediction by threading methods: Evaluation of current techniques. Proteins 23:337-355, 1995.
18. Milosavljević, A., Jurka, J. Discovering simple DNA sequences by the algorithmic similarity method. CABIOS 9:407-411, 1993.
19. NRP (Non-Redundant Protein) Database. Distributed on the Internet via anonymous FTP from ftp.ncifcrf.gov, under the auspices of the National Cancer Institute's Frederick Biomedical Supercomputing Center.
20. Rost, B. Phd: Predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol. 2666: 525-39, 1996.
21. Santner, T.J., Duffy, D.E. "The Statistical Analysis of Discrete Data." Springer Verlag, New York, 1989.
22. Schneider, R., Sander, C. The HSSP database of protein structure-sequence alignments. NAR 24:201-205, 1996.
23. Sippl, M. Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol. 5:229-235, 1995.
24. Sjölander, K., Karplus, K., Brown, M.P., Hughey, R., Krogh, A., Mian, I.S., Haussler, D. Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology. CABIOS 12:327-345, 1996.