Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments.
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ABSTRACT:
SUBMITTER: Xie L
PROVIDER: S-EPMC2291117 | biostudies-literature | 2008 Apr
REPOSITORIES: biostudies-literature
Publications
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments.
Proceedings of the National Academy of Sciences of the United States of America 20080402 14
Here, a scalable, accurate, reliable, and robust protein functional site comparison algorithm is presented. The key components of the algorithm consist of a reduced representation of the protein structure and a sequence order-independent profile-profile alignment (SOIPPA). We show that SOIPPA is able to detect distant evolutionary relationships in cases where both a global sequence and structure relationship remains obscure. Results suggest evolutionary relationships across several previously ev ...[more]
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