Detecting evolutionary relationships across existing fold space, using sequence order-independent profile–profile alignments
- 8 April 2008
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 105 (14) , 5441-5446
- https://doi.org/10.1073/pnas.0704422105
Abstract
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 evolutionary distinct protein structure superfamilies. SOIPPA, along with an increased coverage of protein fold space afforded by the structural genomics initiative, can be used to further test the notion that fold space is continuous rather than discrete.Keywords
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