I am working on research project for virtual screening of several ligands and proteins, and I have to compare protein- ligand interaction (using Autodock) results with protein- protein interaction(HADDOCK) results.
so is it reasonable to compare the results of those different simulations of different softwares ?
I don't think it is reasonable. The complexity of the protein-ligand and protein-protein docking problem is quite different. You can compare the results between the programs using the same data, i. e, the performance of the Autodock and Haddock on the same set of protein-ligand complexes and also on the same data set of protein-proteins. Only then are the problems comparable.
It is not about software.
What is there to compare protein small molecule with protein-protein interaction?
Thanks Prof- Amit for your concern, I was about to compare the therapeutic effect of drug which is protein with another drug which is a ligand using binding affinity as a point of comparison. but both the simulation tools and the type of simulation are different and complex so this was the problem.
Amit V Pandey
Then just use Autodock. Autodock-VINA is more suitable for protein-small molecule docking. Although a direct comparison like virtual binding affinity etc. may be pointless here, it will at least start with the same software/parameters.
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