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Bioinformatics Advance Access published online on April 8, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth247
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received November 10, 2003
Revised February 3, 2004
Accepted February 24, 2004

Applications note

An interactive triple-helical collagen builder

Jan K. Rainey 1* M. Cynthia Goh 2

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

* To whom correspondence should be addressed. E-mail: jrainey{at}biochem.ualberta.ca; jan.rainey@utoronto.ca..


  Abstract

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 Builder 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.


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