SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences

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, coiled coils are quite straightforward and readily recognized via the conspicuous heptad repeats of hydrophobic and polar residues. However, structurally they are more complicated, existing in a range of oligomer states and topologies. Here, we address the issue of predicting coiled-coil oligomeric state from protein sequence. RESULTS: The predominant coiled-coil oligomer states in Nature are parallel dimers and trimers. Here, we improve and retrain the first-published algorithm, SCORER, that distinguishes these states, and test it against the current standard, MultiCoil. The SCORER algorithm has been revised in two key respects: first, the statistical basis for SCORER is improved markedly. Second, the training set for SCORER has been expanded and updated to include only structurally validated coiled coils. The result is a much-improved oligomer state predictor that outperforms MultiCoil, particularly in assigning oligomer state to short coiled coils, and those that are diverse from the training set. AVAILABILITY: SCORER 2.0 is available via a web interface at http://coiledcoils.chm.bris.ac.uk/Scorer. Source code, training sets and Supporting Information can be downloaded from the same site.