Dear Golam, first you can identify missense mutations occurs at gene level (SNPs) and amino acid mutations by using dbsnp available on NCBI. Then use Provean, SIFT, Polyphen, I-mutant to predict the effect of missense mutations on both protein structure and function.

Golam sarwar, You can use PYMOL software for protein visualization and also highlight the mutations in the mutant protein through different representation or colors on that particular amino acid (mutant one).

Thanks Mohd Muzammil Khan. I did that. I wanted to see that if the mutation have the effect on protein structure, or not?I dindt found any change of structure on pymol.Its look like same as wild type protein.

Hi Golam,

It is recommended that you analyze the effect of the mutation site on the structure based on the properties of the target protein, but no prediction software can ensure the true state. If you think it is necessary, you can try structural biology methods, such as X-ray crystallography, NMR, Cryo-electron microscopy, and using experimental methods to determine the structure of proteins is the most convincing.

Hope it helps!

Hi, If your interest is to know the effect of mutation only by in silico, then Molecular Dynamics (MD) simulation can be useful. If you are studying an enzyme having a catalytic role, then biochemical assay can be the first step of characterization. Though mutation can cause a loss of activity or can decrease the activity or bring a new function. Also these mutation may results into change in secondary structure which can be tracked by CD measurements while structure determination can provide insight at atomic level.