Affordable Access

Evaluation of local structure alphabets based on residue burial.

Authors
Type
Published Article
Journal
Proteins Structure Function and Bioinformatics
Publisher
Wiley (John Wiley & Sons)
Volume
55
Issue
3
Pages
508–508
Source
UCSC Bioengineering biomedical-ucsc
License
Unknown

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.

Report this publication

Statistics

Seen <100 times