I want to get the accessible surface area for each residue of a protein structure. I need to do that for biological assembly and remove ligands. I hope this could cover all proteins in UniProt. However, I don't have an efficient way to remove ligands. I have data from SIFTS(http://www.ebi.ac.uk/pdbe/docs/sifts/), which maps PDB residue to UniProt residue. What I am thinking is:
1) I calculate ASA/RSA for all PDBs(Biological Assembly)
2) I take the maximum ASA for all corresponding residues, and assign the maximum ASA to the residue on UniProt
Is this a right way to do it? Because, here I assume, I will always find a PDB without any ligand for each protein in UniProt.
I am thinking to use DSSP or NACCESS. I hope these two tools can deal with water and other molecule correctly.