Hello everyone,
I would like to get help about finding any server or application which can give me info about free energy and dissociation constant of protein-protein docking outputs. I have docked a trimeric form of protein with a single-chain peptide of 37 aa. Please help.
Thank you.
Hi! If you're starting out with protein-protein docked complexes, I'd recommend the PRODIGY web-service to determine binding free energies.
Link: https://wenmr.science.uu.nl/prodigy/
You can try vina --score_only function or epdb option in AutoDock to estimate binding free energies of your protein-peptide complex using the forefields implemented in those programs. See this link (https://sebastianraschka.com/Articles/2014_autodock_energycomps.html) for the details on how to do it. In my experience, AutoDock underestimates the binding energies a little. Vina scoring is more close to the values obtained by UV-Vis spectroscopic experiments.
Once you get the binding free energy, you can obtain the equilibrium constant using the DG = -RT ln Keq relation.
Hej Ajay,
what about the FoldX application? I guess, that would also work.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Peptides