In search for more accurate alignments in the twilight zone.

ABSTRACT: A major bottleneck in comparative modeling is the alignment quality; this is especially true for proteins whose distant relationships could be reliably recognized only by recent advances in fold recognition. The best algorithms excel in recognizing distant homologs but often produce incorrect alignments for over 50% of protein pairs in large fold-prediction benchmarks. The alignments obtained by sequence-sequence or sequence-structure matching algorithms differ significantly from the structural alignments. To study this problem, we developed a simplified method to explicitly enumerate all possible alignments for a pair of proteins. This allowed us to estimate the number of significantly different alignments for a given scoring method that score better than the structural alignment. Using s

SUBMITTER: Jaroszewski L 

PROVIDER: S-EPMC2373660 | biostudies-literature | 2002 Jul

REPOSITORIES: biostudies-literature