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Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm

Type of publication Not peer-reviewed
Publikationsform Original article (non peer-reviewed)
Author Bliven Spencer, Lafita Aleix, Rose Peter, Capitani Guido, Prlić Andreas, Bourne Philip,
Project C16.0072: Discovering evolutionary innovations by assessing variation and natural selection in protein tandem repeats
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Original article (non peer-reviewed)

Journal Biorxiv
Page(s) 1
Title of proceedings Biorxiv
DOI 10.1101/297960

Open Access

Abstract

Many proteins fold into highly regular and repetitive three dimensional structures. The analysis of structural patterns and repeated elements is fundamental to understand protein function and evolution. We present recent improvements to the CE-Symm tool for systematically detecting and analyzing the internal symmetry and structural repeats in proteins. In addition to the accurate detection of internal symmetry, the tool is now capable of i) reporting the type of symmetry, ii) identifying the smallest repeating unit, iii) describing the arrangement of repeats with transformation operations and symmetry axes, and iv) comparing the similarity of all the internal repeats at the residue level. CE-Symm 2.0 helps the user investigate proteins with a robust and intuitive sequence-to-structure analysis, with many applications in protein classification, functional annotation and evolutionary studies. We describe the algorithmic extensions of the method and demonstrate its applications to the study of interesting cases of protein evolution.
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