An automated method for consistent helix assignment using turn information
Article first published online: 1 MAR 2011
Copyright © 2011 Wiley-Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Volume 79, Issue 5, pages 1416–1426, May 2011
How to Cite
Koch, O. and Cole, J. (2011), An automated method for consistent helix assignment using turn information. Proteins, 79: 1416–1426. doi: 10.1002/prot.22968
- Issue published online: 12 APR 2011
- Article first published online: 1 MAR 2011
- Accepted manuscript online: 13 DEC 2010 04:39PM EST
- Manuscript Accepted: 3 DEC 2010
- Manuscript Revised: 30 NOV 2010
- Manuscript Received: 20 JUN 2010
- secondary structure elements;
- automated helix assignment;
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. Proteins 2011; © 2011 Wiley-Liss, Inc.