RT Journal Article
SR Electronic
T1 Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 297960
DO 10.1101/297960
A1 Spencer E Bliven
A1 Aleix Lafita
A1 Peter W Rose
A1 Guido Capitani
A1 Andreas Prlić
A1 Philip E Bourne
YR 2018
UL http://biorxiv.org/content/early/2018/04/09/297960.abstract
AB 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.Availability CE-Symm is an open source tool integrated into the Bio-Java library (www.biojava.org) and freely available at https://github.com/rcsb/symmetry.