Hello everyone,
I am currently studying DNA-protein complexes using Discovery Studio, and I have a few questions regarding the methods:
- I am using the "Prepare Protein" tool to prepare the complex. Is this approach suitable, or does Discovery Studio include a force field for nucleic acids as well?
- Is it feasible to perform ZDock between DNA and protein in Discovery Studio and obtain reasonable results?
- I would like to quantify the binding free energy between the DNA and protein. Could anyone suggest which tools in Discovery Studio would be best for this? I was considering using SMD and FEP calculations, but I’m concerned there may be errors because the ligand is not a small chemical compound.
Thank you in advance for your help!
