You can try I-tasser (number 1 server for protein structure prediction). Have to check about phosphorylation changes

http://zhanglab.ccmb.med.umich.edu/I-TASSER/

Any software for protein modelling or energy minimization may be used like AMBER, CHARMS. These software only work when you wants to mutate few residues.

Hi, are these software free? Could they also simulate phosphorylation-induced structural change? Cheers

You can try I-tasser (number 1 server for protein structure prediction). Have to check about phosphorylation changes

http://zhanglab.ccmb.med.umich.edu/I-TASSER/

For a detailed analysis, Molecular Dynamics Simulations is the preferred one.

U can try out change in secondary structure using dssp, I am using gromacs for the task.

Phosphorylation prediction

http://www.cbs.dtu.dk/services/NetPhosK/