title: Evaluation of local structure alphabets based on residue burial.
abstract: 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 A-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.
authors.affiliation: Department of Biopharmaceutical Sciences, University of California, San Francisco 94143-2240, USA. rachelk@salilab.org
authors.forename: Rachel
authors.initials: R
authors.lastname: Karchin
authors.forename: Melissa
authors.initials: M
authors.lastname: Cline
authors.forename: Kevin
authors.initials: K
authors.lastname: Karplus
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D017124:Conserved Sequence; D008390:Markov Chains; D015394:Molecular Structure; D011487:Protein Conformation; D017510:Protein Folding; D020539:Sequence Analysis, Protein; D012997:Solvents / Q000737:chemistry
chemical_list: D000596:Amino Acids; D012997:Solvents