The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information.
The Predikin webserver allows users to predict substrates of protein kinases. The Predikin system is built from three components: a database of protein kinase substrates that links phosphorylation sites with specific protein kinase sequences; a perl module to analyse query protein kinases and a web interface through which users can submit protein kinases for analysis. The Predikin perl module provides methods to (i) locate protein kinase catalytic domains in a sequence, (ii) classify them by type or family, (iii) identify substrate-determining residues, (iv) generate weighted scoring matrices using three different methods, (v) extract putative phosphorylation sites in query substrate sequences and (vi) score phosphorylation sites for a given kinase, using optional filters. The web interface provides user-friendly access to each of these functions and allows users to obtain rapidly a set of predictions that they can export for further analysis. The server is available at http://predikin.biosci.uq.edu.au.
Saunders
Neil F W
NF
School of Molecular and Microbial Sciences, University of Queensland, Brisbane 4072, Australia. n.saunders@uq.edu.au
Kobe
Bostjan
B
D020134:Catalytic Domain; D020407:Internet; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D010766:Phosphorylation; D011494:Protein Kinases / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D020539:Sequence Analysis, Protein; D012984:Software; D013379:Substrate Specificity
D010455:Peptides; D011494:Protein Kinases