Using a crystal of a complex to guide docking of a mutant


I am working with a complex that is already crystalized. I just modelled a mutant of one of the chains and wanted to test how that will affect the binding interface. Can I use the crystal structure to guide the docking?


And what would be the difference compared to just aligning my model to the crystal structure of the complex?

You could also simply input the mutation in the crystal structure (simply change the residue name, don’t bother deleting / adding atoms) and run it through the refinement server of haddock

And for comparison also run the WT structure through the refinement interface

You can of course use the crystal interface information to do a full docking. But not sure this will add much more.

And there are plenty of other software tools and servers to asses the impact of a mutation on a complex (i.e. a ddG prediction)

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Got it! Thanks. Will try that. Altough my mutant is more than just a point mutation but a whole domain that was replaced by a consensus sequence so the homology of the synthetic protein with extant WT sequence is around 70%. Overall fold is retained but there are differences in loops that mediate binding. I tried docking from scratch but didn’t work so well.