Supposing that we have 1a05.pdb. So chainA is the receptor chain and chainB is the ligand chain. How can we determine the binding site from chainA?
What is the cutoff distance that the atoms from receptor chain must have from the antigen chain in order to find the binding site atoms?
ps: I do also know that these atoms have to be on the Surface of the receptor, so first we have to create a 3D grid around the receptor's protein.
Supposing that we have 1a05.pdb. So chainA is the receptor chain and chainB is the ligand chain. How can we determine the binding site from chainA?
What is the cutoff distance that the atoms from receptor chain must have from the antigen chain in order to find the binding site atoms?
ps: I do also know that these atoms have to be on the Surface of the receptor, so first we have to create a 3D grid around the receptor's protein.