Biasing Scoring Weights
|Opened on:||Monday, April 16, 2012 - 05:30|
|Last modified:||Friday, April 20, 2012 - 00:03|
Sorry if this already exists, but:
To my eye in 540, if others are getting similar results to me, it seems as though too much weight is given to intramolecular bonds, which don't contributing to the affinity between the two proteins. I think it would be a good beneficial for these "design the interface" types of puzzles to "bonus points" or have a multiplication factor for bonds, or especially hydrophobic interactions, which contribute to intermolecular binding.
The Janeway Immuno book also says that antibody-antigen binding surfaces, more than ordinary protein - protein interactions, have a high propensity for aromatic residues.
For the antibody, or small inhibitory peptide design puzzles, another good biasing measure may be to increase the weight given to intermolecular "packing" and "hiding" scores.