So, Thomas, you don't see anything wrong in the way I compute the surfaces?
The numbers should be like that, right?
The reason I need both the molecular surface and the SASA in not directly
related to a physical quantity. I do SQM scoring of compounds bound to
proteins, but the bulkier molecules,
Hi Thomas and Blaine,
SASA is probably the correct feature to evaluate here, not molecular surface.
Of course it may depend the actual goal of this exercise, but typically when
talking about interface surface, you're putting that into context with binding
energy or solvation effects, and only
Hi Thomas,
If you display the SASA of the protein in PyMOL's viewport,
you will see that it and that of the ligand have huge overlaps
How do you define the interface in such a situation and how
do you interpret it?
The interface of the molecular surfaces seems easier to interpret.
Best
