Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments

by: Lei Xie, Philip E Bourne

Proceedings of the National Academy of Sciences, Vol. 105, No. 14. (8 April 2008), pp. 5441-5446.

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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 profileprofile 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. 10.1073/pnas.0704422105

@article{citeulike:2643425, 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 profileprofile 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. 10.1073/pnas.0704422105}, author = {Xie, Lei and Bourne, Philip E. }, citeulike-article-id = {2643425}, doi = {http://dx.doi.org/10.1073/pnas.0704422105}, journal = {Proceedings of the National Academy of Sciences}, keywords = {alignment, evolution, profile, sequence, structure}, month = {April}, number = {14}, pages = {5441--5446}, posted-at = {2008-04-09 03:58:23}, priority = {2}, title = {Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments}, url = {http://dx.doi.org/10.1073/pnas.0704422105}, volume = {105}, year = {2008} }

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TY - JOUR ID - citeulike:2643425 L3 - citeulike-article-id:2643425 TI - Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments JF - Proceedings of the National Academy of Sciences VL - 105 IS - 14 SP - 5441 EP - 5446 N2 - 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 profileprofile 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. 10.1073/pnas.0704422105 KW - alignment KW - evolution KW - profile KW - sequence KW - structure AU - Xie, Lei AU - Bourne, Philip PY - 2008/04/08/ UR - http://dx.doi.org/10.1073/pnas.0704422105 ER -

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