title: SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  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.
authors.affiliation: School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
authors.forename: Craig T
authors.initials: CT
authors.lastname: Armstrong
authors.forename: Thomas L
authors.initials: TL
authors.lastname: Vincent
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Green
authors.forename: Derek N
authors.initials: DN
authors.lastname: Woolfson
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D020407:Internet; D055503:Protein Multimerization; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins