HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins.

  title={HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins.},
  author={Christopher Bystroff and Vesteinn Thorsson and David Baker},
  journal={Journal of molecular biology},
  volume={301 1},
We describe a hidden Markov model, HMMSTR, for general protein sequence based on the I-sites library of sequence-structure motifs. Unlike the linear hidden Markov models used to model individual protein families, HMMSTR has a highly branched topology and captures recurrent local features of protein sequences and structures that transcend protein family boundaries. The model extends the I-sites library by describing the adjacencies of different sequence-structure motifs as observed in the… CONTINUE READING
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