hello everybody,
i see there's no bsp-slim board, so i post here.
my question is of a general nature. most docking algorithms dock ligands, be it either small molecules or peptides or proteins to the SURFACES of the receptors (usually proteins). But in many cases, the binding cavity is in the INTERIOR of the receptor and docking algorithms have no clue as to how to get in there. except AutoDock, in which a box can be defined at a presumed internal site in order to orient the ligand for docking, I know of no other algorithm that can do that. BSP seems to be docking also at the surface of the receptor. is there not a way to adress this issue in bsp ? can bsp dock peptides to proteins ? what's the maximum length allowed for the peptides ?
Greetings,
C Maroun