LOGICOIL—multi-state prediction of coiled-coil oligomeric state

Vincent, Thomas L.
Green, Peter J.
Woolfson, Derek N.

¹School of Chemistry, University of Bristol, Bristol BS8 1TS, ²Bristol Centre for Complexity Science, University of Bristol, Bristol BS8 1TR, ³School of Mathematics, University of Bristol, Bristol BS8 1TW and ⁴School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK

*To whom correspondence should be addressed.

Associate Editor: Alfonso Valencia

Received May 15, 2012

Accepted October 26, 2012

Bioinformatics 29(1):p 69-76, January 2013. | DOI: 10.1093/bioinformatics/bts648

Motivation: The coiled coil is a ubiquitous α-helical protein-structure domain that directs and facilitates protein–protein interactions in a wide variety of biological processes. At the protein-sequence level, the coiled coil is readily recognized via a conspicuous heptad repeat of hydrophobic and polar residues. However, structurally coiled coils are more complicated, existing in a wide range of oligomer states and topologies. As a consequence, predicting these various states from sequence remains an unmet challenge.

Results: This work introduces LOGICOIL, the first algorithm to address the problem of predicting multiple coiled-coil oligomeric states from protein-sequence information alone. By covering >90% of the known coiled-coil structures, LOGICOIL is a net improvement compared with other existing methods, which achieve a predictive coverage of ∼31% of this population. This leap in predictive power offers better opportunities for genome-scale analysis, and analyses of coiled-coil containing protein assemblies.

Availability: LOGICOIL is available via a web-interface at http://coiledcoils.chm.bris.ac.uk/LOGICOIL. Source code, training sets and supporting information can be downloaded from the same site.

Contact:[email protected]

Supplementary information: Supplementary data are available at Bioinformatics online.