Acknowledgments
Authors
This facility is the work of David P. Leader and the late E. James Milner-White of the School of Life Sciences in the University of Glasgow, UK. In any published work arising from the use of this facility please cite ‘Leader and Milner-White, BMC Bioinformatics (2009) 10:60’ and the following url:
http://motif.mvls.gla.ac.uk
Contributors
The following students from the Glasgow University M.Res. course in Bioinformatics have contributed to this facility during 15-week summer projects: Fang Chen, Simon Harding, Suraj Menon, Christopher Tindal, Meng-Pin Weng, Chintan Vora and Shrikant Sharma.
Data and Programs used in the database
- The database underlying this facility uses the ‘Top 500’ versions of the public PDB files
(http://kinemage.biochem.duke.edu/databases/top500.php). - The program, HBPlus, was used to determine hydrogen bonds.
(McDonald and Thornton, J.Mol.Biol. 238:777-793,1994) - The program, DSSP, was used to determine dihedral angles and secondary structure.
(Kabsch and Sander, Biopolymers 2:2577-2637, 1983) - The program, BBDEP, was used to determine side-chain angles.
(Dunbrack and Karplus, J.Mol.Biol. 230:543-571, 1993.)
Two-dimensional Graphics
The program used to generate the two-dimensional secondary-structure graphics is ‘SecondGlance’ by David P. Leader (available from the author). It owes its visual inspiration to the ‘Wirplot’ diagrams of Roman Laskowski (see e.g. Laskowski et al., Nucleic Acids Res. 33:D266-D268, 2005). Please acknowledge ‘SecondGlance’ in any publication using images generated by the program.
Three-dimensional Graphics
The program JSmol (http://wiki.jmol.org/index.php/JSmol/), was used for the interactive three dimensional graphics. Users wishing to learn more about JSmol may find the Wiki (http://wiki.jmol.org/) a useful starting point.
Lookup Facility
The protein ID lookup is performed using the PDBSum SearchHeaders.pl facility at EBI, Cambridge. We thank Roman Laskowski for his cooperation in this regard.
Graphics in the Motif Glossary
Graphics in the Motif Glossary were generated by, and are the property of, the authors. They should not be used in any other web pages or in print without first obtaining written permission. This will normally be granted, given suitable use with proper attribution.