jkleinj / symmetry

:ferris_wheel: Detect, analyze, and visualize protein symmetry

Symmetry in Biomolecular Structures

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.

Tools

User interfaces are available within the symmetry-tools module.

CE-Symm

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.

When using CE-Symm, please cite:

CE-Symm version 2:

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.

CE-Symm version 1:

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.

Quaternary Symmetry

The QuatSymm tool is used for identifying quaternary symmetry in protein complexes. It is also able to tolerate mutations and detect pseudosymmetry in complexes with structurally homologous subunits. See QuatSymm documentation for more details.

The QuatSymm algorithms are used by the RCSB Protein Data Bank's quaternary symmetry analysis. The tool was also utilized for biological assembly assessment during the 12th Critical Assessment of Structure Prediction in 2016.

Dependencies

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.

Building

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.