[gmx-users] Re : Simulation for prediction of binding between a peptide and protein

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 11 14:32:28 CEST 2011

> Hi,
> I want to know how can I predict where a designed peptide will bind to 
> my protein target or not using simulation ... Can anybody guide me ??

I don't think anybody has the computational resources to answer this 
question with unguided MD. Docking programs are probably the way to get 
a guide about what binding modes might be reasonable, but I don't know 
what software might be fit for the purpose.


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