A comparative study of available software for high-accuracy homology modeling: from sequence alignments to structural models.

ABSTRACT: An open question in protein homology modeling is, how well do current modeling packages satisfy the dual criteria of quality of results and practical ease of use? To address this question objectively, we examined homology-built models of a variety of therapeutically relevant proteins. The sequence identities across these proteins range from 19% to 76%. A novel metric, the difference alignment index (DAI), is developed to aid in quantifying the quality of local sequence alignments. The DAI is also used to construct the relative sequence alignment (RSA), a new representation of global sequence alignment that facilitates comparison of sequence alignments from different methods. Comparisons of the sequence alignments in terms of the RSA and alignment methodologies are made to better understand

SUBMITTER: Nayeem A 

PROVIDER: S-EPMC2242473 | biostudies-literature | 2006 Apr

REPOSITORIES: biostudies-literature