Hello,
I am looking to calculate the binding free energy between two proteins. I am looking for the most widely accepted and rigorous method. I was thinking about using FEP. However, I noticed very few papers that use this method in protein-protein interactions, and it is mainly used for protein-ligand binding.
Could someone guide me on how to go about applying FEP or maybe an alternative but rigorous method for protein-protein binding affinity calculations.
In free energy calculations, the probe can be anything (including an amino acid residue at the protein-protein interface). Free energy perturbation is the most rigorous method; linear interaction energy (LIE) is its cheaper alternative:
Article Probing the Effect of Point Mutations at Protein-Protein Int...
Thank you. I was just worried about sampling and the time scale that would be required since it is a larger system.
It might not be necessary to include the entire protein-protein complex in the simulated system. In the paper i mentioned: radius of the simulation sphere, 16 Angstroms; production time, 225 ps; energy sampling, every 5th step. They judged the convergence "by dividing the trajectory in two halves and then calculating the free energy for each of these two halves. If this energy differs by >2.0 kcal/mol, the simulation was further extended (up to 750 ps in a few cases). This also provides an estimate of the convergence error in the computed binding energies, which is on average
- Badges
- Science topic
- Similar topics
- Cognitive Science
- Thinking