Context-specific amino acid substitution matrices and their use in the detection of protein homologs.

@article{Goonesekere2008ContextspecificAA,
  title={Context-specific amino acid substitution matrices and their use in the detection of protein homologs.},
  author={Nalin C. W. Goonesekere and Byungkook Lee},
  journal={Proteins},
  year={2008},
  volume={71 2},
  pages={910-9}
}
The sequence homology detection relies on score matrices, which reflect the frequency of amino acid substitutions observed in a dataset of homologous sequences. The substitution matrices in popular use today are usually constructed without consideration of the structural context in which the substitution takes place. Here, we present amino acid substitution matrices specific for particular polar-nonpolar environment of the amino acid. As expected, these matrices [context-specific substitution… CONTINUE READING