This project collects tools to detect, analyze, and visualize protein symmetry. This includes the CE-Symm tool for internal symmetry, a tool for quaternary symmetry, and other experiments relating to symmetry.
This project serves dual purposes. First, it acts as an incubator for new methods and contains RCSB-specific or other non-production ready code. Stable methods have been moved to the biojava library, where they are accessible for programatic use. Second, user interfaces are built here following each BioJava release. See releases for the latest CE-Symm executable.
User interfaces are available within the symmetry-tools module.
CE-Symm is a tool for detecting internal symmetry in protein structures. CE-Symm version 2 is able to detect both open and closed symmetry and provide a multiple alignment of all repeats.
See CE-Symm documentation for more details on how to use the tool.
If you find CE-Symm useful for your research, please consider citing:
Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm
Spencer E Bliven, Aleix Lafita, Peter W Rose, Guido Capitani, Andreas Prlić, & Philip E Bourne
PLOS Computational Biology (2019) 15 (4):e1006842.
Systematic detection of internal symmetry in proteins using CE-Symm
Douglas Myers-Turnbull, Spencer E Bliven, Peter W Rose, Zaid K Aziz, Philippe Youkharibache, Philip E Bourne, & Andreas Prlić
J Mol Biol (2013) 426 (11): 2255–2268.
The QuatSymm tool is used for identifying quaternary symmetry in protein complexes. It is also able to detect pseudosymmetry in complexes with structurally homologous subunits. The QuatSymm tool is used by the RCSB Protein Data Bank's quaternary symmetry analysis and it has also been utilized to assess protein assembly predictions at CASP challenges.
See QuatSymm documentation for more details.
If you find the QuatSymm tool useful for your research, please consider citing the following publications where it has been described:
BioJava 5: A community driven open-source bioinformatics library
Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, Jose M. Duarte
PLOS Computational Biology 15(2): e1006791
This project requires Java 1.8 or newer. Release versions of all tools can be run with no other dependencies.
To build from source, the library requires Apache Maven.
Additional dependencies (BioJava, Jmol, etc) should be automatically resolved by Maven.
To build, run
mvn package
This will build the CE-Symm release packages (e.g. symmetry-tools/target/cesymm-X.X.X.jar) and jar files containing the other code.