nioroso-x3
commented
5 years ago Sorry for taking so long, LIGAND <--- PROTEIN is the value you need. It indicates how much of the ligand surface is buried by the protein. The arrow indicates that PROTEIN is burying surface from LIGAND. The interface is the average from the buried surfaces of a object pair. Also I'm not a Doctor! (yet)
Dear Dr Judemir Ribeiro,
I'm pretty interested in your recently published tool dr-sasa, which can be used to calculate solvent-accessible surface area (SASA).
In my study, I want to calculate the solvent-accessible surface area of the ligand molecule that is buried upon binding (ΔSAS). So I read the instructions at your Github page, and I guess "mode 1" should be appropriate for my purpose because this mode calculatess the delta SASA (change in Solvent Accessible Surface Area) or BSA in various objects contained in a single pdb or mol2 file.
My input pdb file contains one protein chain only (chain A) and one ligand only (residue name: T27. Also on chain A). Running dr-sasa (./dr_sasa -m 1 -i 2zd1.pdb) generated the following output:
Selected complex surface (A^2): 30640.3 Object LIGAND complexed surface (A^2): 32.8962 Object PROTEIN complexed surface (A^2): 30607.4 Object LIGAND uncomplexed surface (A^2): 614.248 Object PROTEIN uncomplexed surface (A^2): 30905 LIGAND <--- PROTEIN buried surface (A^2): 581.352 LIGAND ---> PROTEIN buried surface (A^2): 297.625 Interface LIGAND/PROTEIN (A^2): 439.489
My question is, which value is the SASA of the ligand that is bured upon binding (ΔSAS)? Could you briefly explain to me how to interpret the last three rows? Thank you.