Rapid search for tertiary fragments reveals protein sequence-structure relationships.

ABSTRACT: Finding backbone substructures from the Protein Data Bank that match an arbitrary query structural motif, composed of multiple disjoint segments, is a problem of growing relevance in structure prediction and protein design. Although numerous protein structure search approaches have been proposed, methods that address this specific task without additional restrictions and on practical time scales are generally lacking. Here, we propose a solution, dubbed MASTER, that is both rapid, enabling searches over the Protein Data Bank in a matter of seconds, and provably correct, finding all matches below a user-specified root-mean-square deviation cutoff. We show that despite the potentially exponential time complexity of the problem, running times in practice are modest even for queries with many

SUBMITTER: Zhou J 

PROVIDER: S-EPMC4380982 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature