To assess protein stability you could try molecular dynamics based approach (doi:10.1016/j.bpj.2010.01.051) or Rosetta based calculation (DOI:10.1002/prot.22921).

To predict pKa shifts an alchemical MD approach could be taken similarly to that of protein thermostability calculations. Another way is to use an empirical predictor, e.g. Propka (DOI: 10.1021/ct100578z)

For aggregation prediction could try Tango (doi:10.1038/nbt1012) or Zyggregator (doi:10.1016/j.jmb.2008.05.013).

Thanks Gapsys

Could you kindly help me in analyzing the data

there are no. of tools are their to check the stability of proteins, majorly Gromacs, NAMD, are most popular ones. Regarding pka and aggregation prediction i agree with the tools suggested by Gapsys

If you have a 3D structure of your protein, you can analyse the difference in stability of any mutant with FoldX, which is similar to Cupstat. Here is the website:

http://foldx.crg.es/

Don't hesitate to contact me if you need more help.