Analysis of protein homology by assessing the (dis)similarity in protein loop regions.

ABSTRACT: Two proteins are considered to have a similar fold if sufficiently many of their secondary structure elements are positioned similarly in space and are connected in the same order. Such a common structural scaffold may arise due to either divergent or convergent evolution. The intervening unaligned regions ("loops") between the superimposable helices and strands can exhibit a wide range of similarity and may offer clues to the structural evolution of folds. One might argue that more closely related proteins differ less in their nonconserved loop regions than distantly related proteins and, at the same time, the degree of variability in the loop regions in structurally similar but unrelated proteins is higher than in homologs. Here we introduce a new measure for structural (dis)similarity i

SUBMITTER: Panchenko AR 

PROVIDER: S-EPMC1994810 | biostudies-literature | 2004 Nov

REPOSITORIES: biostudies-literature