FORESST: A Selected Bibliography
- 1999: V. Di Francesco, P.J. Munson, and J. Garnier, "FORESST:
fold recognition from secondary structure predictions of proteins,"
Bioinformatics, vol. 15, pp. 131- 140.
- 1999: V. Geetha, Valentina di Francesco, Jean Garnier, and
Peter J. Munson, "Comparing protein sequence-based and predicted
secondary structure-based methods for identification of
remote homologs," Protein Engineering, vol. 12, pp. 527 - 534.
- 1997: Valentina Di Francesco, V. Geetha, Jean Garnier, and Peter
J. Munson, "Fold Recognition Using Predicted Secondary Structure Sequences
and Hidden Markov Models of Protein Folds," PROTEINS: Structure, Function,
and Genetics, Suppl. 1, pp. 123-128.
- 1997: Valentina Di Francesco, Jean Garnier, and Peter J. Munson,
"Protein topology recognition from secondary structure sequences: Applications
of the hidden Markov models to the alpha class porteins," Journal of
Molecular Biology, vol. 267, pp. 446-463.
- 1997: C.A. Orengo, A. D. Michie, S. Jones, D.T. Jones,
M.B. Swindells, and J. M. Thornton, "CATH- A Hierarchic Classification of
Protein Domain Structures," Structure, Vol 5. No 8. p.1093-1108.
- 1996: Richard Hughey, Anders Krogh, Christian Barrett, and
Leslie Grate, "SAM Sequnce Alignment and Modeling Software System,"
University of California, Santa Cruz, Technical Report
UCSC-CRL-95-7. (NOTE: This report is valid for the version of
SAM used by FORESST.)
- 1994: 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, vol. 235,
pp. 1501 - 1531.
- 1989: Lawrence R. Rabiner, "A Tutorial on Hidden Markov Modles and
Selected Applications in Speech Recognition," Proceedings of the IEEE,
vol. 77, no. 2, pp. 257 - 286. (NOTE: A good review of the basics of
hidden Markov models.)
- 1983 W. Kabsch and C. Sander, "Dictionary of protein secondary
structure- pattern- recognition of hydrogen- bonded and geometrical
features," Biopolymers, vol. 22, pp. 2577- 2637.
- 1979 G.E. Schulz and R. H. Schirmer, Principles of Protein
Structure, Springer-Verlage, New York.
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