Server Description

Contact order is a topological descriptor that has been shown to be correlated with several interesting protein properties such as protein folding rates and protein transition state placements. Contact order has also been used to select for viable protein folds from ab initio protein structure prediction programs.

This server has two functions regarding the protein contact order, the primary protein sequence based contact order prediction and protein 3D structure based contact order calculation.

For prediction:

After a sequence is submitted, the server will first run a blast search against a sequence database which contains about 15,000 sequences. If a homology is found , the server will output the contact order calculated based on the 3D structure [2] of the homolog protein. Otherwise, if no homology is identified, the server will use a linear regression formular to predict the contact order mainly based on the secondary structure prediction information generated by Proteus [1].

For calculation:

This server can also perform the protein contact order calculation for a given 3D structure based on the contact order definition proposed in [2] and [3].

 

Notice:

Calculated contact order database for TREMBL dataset added in Supplementary. Contains 15,999,775 sequences. (2012/0104)

The server framework has been re-arranged. (2011/0722)

This server has been upgraded to be able to predict contact order in formulas based on % of secondary structure which may give higher prediction accuracies. So now there are 6 methods: F3_p, F7_p, F27_p, F3_s, F7_s, and F27_s. (2008/03/18)

This server has been upgraded to be able to predict contact order in three formulas, F3, F7, and F27. (2007/11/25)

This server has been moved to a new file system, and the calculation/prediction response time has been highly improved. (2007/10/05)

Currently this server only predict contact order of soluble proteins (membrane proteins are not included). (2007/09/25)

 

References:

[1] Montgomerie S, Sundararaj S, Gallin W, Wishart DS: Improving the accuracy of protein secondary
structure prediction using structural alignment. BMC Bioinformatics 2006, 7:301.

[2] Ivankov DN, Garbuzynskiy SO, Alm E, Plaxco KW, Baker D, Finkelstein AV: Contact order revisited:
Influence of protein size on the folding rate. Protein Science 2003, 13:20572062.

[3] Plaxco KW, Simons KT, Baker D: Contact order, transition state placement and the refolding rates
of single domain proteins. Journal of Molecular Biology 1998, 227:985994.

 

Access count: (Since Oct. 1, 2007)