PT  - JOURNAL ARTICLE
AU  - Spencer E Bliven
AU  - Aleixa Lafita
AU  - Peter W Rose
AU  - Guido Capitani
AU  - Andreas Prlić
AU  - Philip E Bourne
TI  - Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm
AID  - 10.1101/297960
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 297960
4099  - http://biorxiv.org/content/early/2018/10/30/297960.short
4100  - http://biorxiv.org/content/early/2018/10/30/297960.full
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.Availabilit: CE-Symm is an open source tool integrated into the BioJava library(www.biojava.org)and freely available at https://github.com/rcsb/symmetry.