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Bioinformatics Advance Access originally published online on April 8, 2004
Bioinformatics 2004 20(15):2458-2459; doi:10.1093/bioinformatics/bth247
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Bioinformatics 20(15) © Oxford University Press 2004; all rights reserved.

Applications Note

An interactive triple-helical collagen builder

Jan K. Rainey 1,2,* and M. Cynthia Goh 2

1 Protein Engineering Network of Centres of Excellence (PENCE), University of Alberta, Edmonton, AB, T6G 2S2 Canada and 2 Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6 Canada

Received on November 10, 2003; revised on February 3, 2004; accepted on February 24, 2004
Advance Access Publication April 8, 2004

Summary: To facilitate the building of triple-helical polypeptide structures, we provide an interactive, platform-independent Tcl/Tk script. User specified amino acid sequences are parsed to obtain localized melting temperature estimates corresponding to helical propensity. These propensities may be graphically examined prior to their automated use in combination with two separate statistical parameter sets to build the complete polypeptide backbone and, if desired, predict side-chain terminal atom locations.

Availability: The Tcl/Tk Triple Helical collagen Building Script (THe BuScr) and full documentation is freely available under the terms of the GNU General Public License at www.pence.ca/~jrainey/ or www.chem.utoronto.ca/staff/MCG/

Supplementary information: www.pence.ca/~jrainey

Contact: jrainey{at}biochem.ualberta.ca

* To whom correspondence should be addressed.


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