FORESST - FOld REcognition from Secondary STructures

FORESST Release 2.0

Interactive WWW access to FORESST

FORESST is a database (with search engine) of hidden Markov models that characterize secondary structure representations of protein structural domains. The models are based on structural families in the CATH database. At present FORESST consists of 349 models.

What Services Are Available?

Automatic FORESST Search for Possible Folds:
Enter a query sequence as an amino acid sequence and an email will be sent
to you when the calculation is done. This version will automatically predict
the secondary structure using PSI PRED and will retain the hidden Markov model
having the highest significant Z score with a consensus sequence length within
20% of the query sequence length. In this version a significant Z score is a Z
score greater than or equal to 2. Prior a FORESST search, a PSI BLAST search is done automatically on
the query sequence. When homologues of known structure are found, they are
listed and you will be requested to refer to an homology modeling program on the
basis that an homology modeling will be more accurate than a fold prediction.
Manual Alignment using FORESST: Align a query secondary structure sequence against a particular model of a fold family in the FORESST database. (NOTE: this is done on- line. No email sent.)

Before Using FORESST, Kindly Read the Following Information

If results from this server are to used in a publication, please reference this paper: 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.

For a list of other papers pertinent to FORESST, see the bibliography.

How does FORESST score a match between a sequence and a family? See discussion.

Need a secondary structure prediction? Check out this list of Web sites.

The search and alignment engines used by FORESST utilize the Sequence Alignment Modeling (SAM) package developed by the Baskin Center for Computer Engineering and Science, University of California, Santa Cruz.

The FORESST database and Web implementation were developed by Valentina di Francesco, Jason Wilder, P.G. McQueen, Jean Garnier, and Peter Munson as a joint collaboration between The Institute for Genomic Research and the National Institutes of Health.

This Website supported by the Mathematical and Statistical Computing Laboratory and the Scientific Computing Resource Center, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health.

Comments or questions? Send email to P.G. McQueen.

Last updated February 3, 2000.

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