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
a particular model of a fold family in the FORESST database. (NOTE:
this is done on- line. No
- Mainly Alpha Protein Models.
- Mainly Beta Protein Models.
- Alpha/Beta Protein Models.
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
How does FORESST score a match between a sequence and a family? See
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.
Before Using FORESST, Kindly Read the Following Information
Comments or questions? Send email to
Last updated February 3, 2000.
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