Ab Initio server prototype for prediction of phosphorylation sites in proteins

We describe an ab initio server prototype for prediction of phosphorylation sites. A list of possible active sites for a given query protein is build using query protein sequence and the database of proteins annotated for a certain type of activation process by Swiss-Prot DB. All short segments of a query protein sequence centered around plausible active sites are compared with experimental profiles. Those profiles describe both sequence and structure preferences for each type of active site. Prediction of local conformation of a query protein chain around examined site is done with the specially prepared library of short local structural segments (LSSs). The short sequence fragments from a query protein are matched with segments in the library using profile with profile alignment. Predicted local structure of a chain near active site qualitatively agrees with experimental data fetched from PDB data­base. We estimate in this paper the level of improvement over purely sequence based methods gained by incorporating predicted structural information into the local description of phosphorylation sites.