How to observe the structural changes in protein structure for single residue mutation
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9 months ago

I am working on SNP. This is my first approach towards bioinformatics, so I am learning with each step and finding problems as well. After predicting functional SNPs, I am trying to see their direct effect on protein structure. As my protein structure was not available on PDB, I modeled it by GalaxyWEB (SWISS-MODEL is not giving the whole structure, i-tasser & Phyre2 produced low-quality structure- maybe because good templates are not available). Now I have produced the mutant structure by Scwrl4 ( as many people suggested it gives the best side-chain conformation prediction). Now, what should I do with these- should I check only RMSD, TM score and come to the conclusion? Actually I wanted to see more detailed in structural change caused by the deleterious mutations.

SNP Protein structural analysis by mutation • 196 views
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You are unlikely to really be able to see the effect of SNPs on structure through homology modelling. You would need to do proper molecular dynamics.

The best you can do is suggest possible differences in binding etc given whats known about the properties of the new amino acid. You could try providing RMSDs etc, but if your models are poor already, these numbers will be misleading.

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