Evaluation of local structure alphabets based on residue burial

Residue burial, which describes a protein residue's exposure to solvent and neighboring atoms, is key to protein structure prediction, modeling, and analysis. We assessed 21 alphabets representing residue burial, according to their predictability from amino acid sequence, conservation in structural alignments, and utility in one fold-recognition scenario. This follows upon our previous work in assessing nine representations of backbone geometry.(1) The alphabet found to be most effective overall has seven states and is based on a count of C-beta atoms within a 14 Angstrom-radius sphere centered at the C-beta of a residue of interest. When incorporated into a hidden Markov model (HMM), this alphabet gave us a 38% performance boost in fold recognition and 23% in alignment quality. (C) 2004 Wiley-Liss, Inc.