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Article abstractREFERENCEPrediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequenceBlom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S. Proteomics. 2004 Jun;4(6):1633-49. Review.
Center for Biological Sequence Analysis, BioCentrum-DTU,
The Technical University of Denmark, DK-2800 Lyngby, Denmark
ABSTRACT
Post-translational modifications (PTMs) occur on almost all proteins
analyzed to date. The function of a modified protein is often strongly
affected by these modifications and therefore increased knowledge
about the potential PTMs of a target protein may increase our
understanding of the molecular processes in which it takes
part. High-throughput methods for the identification of PTMs are being
developed, in particular within the fields of proteomics and mass
spectrometry. However, these methods are still in their early stages,
and it is indeed advantageous to cut down on the number of
experimental steps by integrating computational approaches into the
validation procedures. Many advanced methods for the prediction of
PTMs exist and many are made publicly available. We describe our
experiences with the development of prediction methods for
phosphorylation and glycosylation sites and the development of
PTM-specific databases. In addition, we discuss novel ideas for PTM
visualization (exemplified by kinase landscapes) and improvements for
prediction specificity (by using ESS - evolutionary stable sites). As
an example, we present a new method for kinase-specific prediction of
phosphorylation sites, NetPhosK, which extends our earlier and more
general tool, NetPhos. The new server, NetPhosK, is made publicly
available at the URL http://www.cbs.dtu.dk/services/NetPhosK/. The
issues of underestimation, over-prediction and strategies for
improving prediction specificity are also discussed.
CORRESPONDENCE
Thomas Sicheritz-Pontén,
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