Using protein design for homology detection and active site searches.

ABSTRACT: We describe a method of designing artificial sequences that resemble naturally occurring sequences in terms of their compatibility with a template structure and its functional constraints. The design procedure is a Monte Carlo simulation of amino acid substitution process. The selective fixation of substitutions is dictated by a simple scoring function derived from the template structure and a multiple alignment of its homologs. Designed sequences represent an enlargement of sequence space around native sequences. We show that the use of designed sequences improves the performance of profile-based homology detection. The difference in position-specific conservation between designed sequences and native sequences is helpful for prediction of functionally important residues. Our sequence sel

SUBMITTER: Pei J 

PROVIDER: S-EPMC208762 | biostudies-literature | 2003 Sep

REPOSITORIES: biostudies-literature