Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility.

ABSTRACT: In comparative modeling, the quality of amino acid sequence alignment still constitutes a major bottleneck in the generation of high quality models of protein three-dimensional (3D) structures. Substantial efforts have been made to improve alignment quality by revising the substitution matrix, introducing multiple sequences, replacing dynamic programming with hidden Markov models, and incorporating 3D structure information. Improvements in the gap penalty have not been a major focus, however, following the development of the affine gap penalty and of the secondary structure dependent gap penalty. We revisited the correlation between protein 3D structure and gap location in a large protein 3D structure data set, and found that the frequency of gap locations approximated to an exponential fu

SUBMITTER: Hijikata A 

PROVIDER: S-EPMC3110861 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature