Hello.
I am docking two proteins and then comparing the results with another docking study where one of the proteins has an SNP.
For the first protein (which is then mutated), there is a motif specifically responsible for interacting with the 2nd protein (obtained from literature and Uniprot). It is 6 amino acids long.
When I first performed docking on HADDOCK, I only selected these 6 amino acids as active residues, and the results that I got for both WT and mutated protein's docking (the docking runs between WT-protein2 and Mutated-protein2) were similar, as in, the scores were pretty much the same. So I am wondering if including a larger portion of protein 1 for docking will give better results. For this purpose, how can I create a grid around that motif of protein 1? Or is there another way I can approach this problem?
Thanking everyone in advance for their help.
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