Protocol for protein:protein binding energy

[A-Frances]

Dear BFEE2 team,

I am using BFEE2 to determine the binding energy between two large proteins (~150 amino acids for the ‘ligand’ and ~400 amino acids for the ‘protein’, respectively). I am using the geometric route although I suspect it does not adequately account for the large conformational variability of the ‘ligand’. Do you know of a way to take this factor into account? Do you recommend the alchemical route instead, or it will also cause problems?

Best regards, Antonio