title: An automated method for consistent helix assignment using turn information.
abstract: A new automated helix assignment method is presented that leads to a more consistent definition of the helix termini, especially of the helix C-terminus. The method assigns a helix to segments of protein chain where adjacent helical turn structures are observed, capped by specific distorted turn types (e.g., open helical turns without a hydrogen bond) or capping motifs (e.g., the Schellman motif). Helix termini are detected by observing the behavior of the NH group in N-termini and the CO group in C-termini; in each case, the respective group must be free to interact with hydrogen bonding partners outside of the putative helix for a helix terminus to be assigned. The presented assignment method and SHAFT-assigned helices are part of Secbase and are made available with Relibase+ 3.0 and the free web version of Relibase 3.0. The method can also be used for the helix assignments of additional protein structures.
authors.affiliation: The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom. oliver.koch@sp.intervet.com
authors.forename: Oliver
authors.initials: O
authors.lastname: Koch
authors.forename: Jason
authors.initials: J
authors.lastname: Cole
mesh_terms: D003198:Computer Simulation; D030562:Databases, Protein; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins