nioroso-x3 / dr_sasa_n Goto Github PK

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.