Detection of circular permutations within protein structures using CE-CP

Spencer E Bliven; Philip E Bourne; Andreas Prlić

doi:10.1093/bioinformatics/btu823

Detection of circular permutations within protein structures using CE-CP

Bioinformatics. 2015 Apr 15;31(8):1316-8. doi: 10.1093/bioinformatics/btu823. Epub 2014 Dec 12.

Authors

Spencer E Bliven¹, Philip E Bourne¹, Andreas Prlić²

Affiliations

¹ Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.
² Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.

Abstract

Motivation: Circular permutation is an important type of protein rearrangement. Natural circular permutations have implications for protein function, stability and evolution. Artificial circular permutations have also been used for protein studies. However, such relationships are difficult to detect for many sequence and structure comparison algorithms and require special consideration.

Results: We developed a new algorithm, called Combinatorial Extension for Circular Permutations (CE-CP), which allows the structural comparison of circularly permuted proteins. CE-CP was designed to be user friendly and is integrated into the RCSB Protein Data Bank. It was tested on two collections of circularly permuted proteins. Pairwise alignments can be visualized both in a desktop application or on the web using Jmol and exported to other programs in a variety of formats.

Availability and implementation: The CE-CP algorithm can be accessed through the RCSB website at http://www.rcsb.org/pdb/workbench/workbench.do. Source code is available under the LGPL 2.1 as part of BioJava 3 (http://biojava.org; http://github.com/biojava/biojava).

Contact: sbliven@ucsd.edu or info@rcsb.org.

Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Algorithms*
Computational Biology / methods*
Databases, Protein*
Dynamins / chemistry*
Humans
Programming Languages
Protein Structure, Tertiary
Sequence Analysis, Protein / methods
Structural Homology, Protein*

Substances

Dynamins

Grants and funding

T32GM8806/GM/NIGMS NIH HHS/United States