Q:

Protein PTM site prediction

Is there any in silico analysis method to predict post-translational modification sites on a given protein? 

A:

There are actually a lot of these sites available, I have used some of the one listed below. Additionally there are some huge list of other services available in this field from ExPASy, you can find it here and the Center for Biological Sequence Analysis, which can be found here.

ExPASy - FindMod
The Eukaryote Linear Motif resource for Functional Sites in Proteins
Phosida

