SitesIdentify


SitesIdentify is a tool that predicts the location of a functional site on the surface of a protein. It predicts PDB coordinates of the centre of the predicted functional site based on locating the peak charge potential on the surface of the protein. If required, this information can be combined with conservation information to provide a more accurate prediction, although this takes more time to compute.

Given a specified radius of this central point, a list of residues residing on the surface of the protein within that radius can be returned. These residues are highlighted on the structure to allow you to view the predicted functional site residues.

The method is described in more detail in background information or in the methods of charge-based predictions or charge and conservation-based predictions.

To submit a job, please go to the SITE PREDICTION section.

SitesIdentify References

Bray, T., Chan, P., Bougouffa, S., Greaves, R., Doig, A., Warwicker., J (2009) SitesIdentify: A funtional site prediction tool. BMC Bioinformatics 10:379.

Greaves, R., Warwicker, J., (2005) Active site identification through geometry-based and sequence profile-based calculations: burial of catalytic clefts. J Mol Biol. 179,125-142.

Bate, P., Warwicker, J., (2004). Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods. J Mol Biol. 340, 263-276.