I want to do simulations analysis for investigating the effect of non-synonymous mutations on protein structure through Discovery Studio. Kindly suggest me a protocol.
INPS is another tool (https://www.ncbi.nlm.nih.gov/pubmed/25957347) for predicting the impact of non-synonymous variations on protein stability from sequence (http://inps.biocomp.unibo.it).
I'm not familiar with Discovery Studio, but Charmm-gui makes running MD simulations of SNPs very easy via their web-interface that generates all the files necessary to run MD for most common packages.
Check it out at: http://charmm-gui.org/?doc=input/mdsetup