HMMSTR ( Hidden Markov Model for Local Sequence-Structur) is a hidden Markov model for protein structure prediction. The program takes as input an amino acid probability distribution (or profile) for each residue position. A profile may be derived from a multiple sequence alignment, or by running the database search program such as PSI_BLAST. It contains the programs needed to predict secondary structure starting with a sequence profile. The sequence profile (a vector of 20 probabilities for each residue in the sequence) can be the output of a profile HMM such as HMMer. It may also be the output of Psi-Blast, which uses profiles internally, or may be generated from a multiple sequence alignment. The programs in this package, HMMSTR and associated format converters, will give you a probabilistic prediction of each of the six DSSP symbols: H,E,G,S,T and _. For now, this is a bare-bones package.
- Fortran compiler
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BMC Bioinformatics. 2008 Oct 10;9:429. doi: 10.1186/1471-2105-9-429.
Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure.
Bystroff C, Webb-Robertson BJ.
Bystroff C, Thorsson V & Baker D. (2000).
HMMSTR: A hidden markov model for local sequence-structure correlations in proteins.
Journal of Molecular Biology 301, 173-90.