dr-sasa is a solvent accessible surface area (SASA) calculation software for biological molecules, which supports proteins, nucleic acids and small organic molecules as inputs. The input files can be provided in either the PDB or Mol2 format. PDB format files will use a NACCESS compatible vdW radii lookup table, while Mol2 formats will use the same VdW radii used in Chimera.
There are five operation modes. The first does common SASA calculations, the second calculates the buried surface area (BSA) between various chains or molecular objects, and third and fourth calculate BSA between residues and atoms as if they were independent objects. The fifth mode calculates BSA without requiring that the atoms are solvent accessible. This mode simply calculates the raw contact surface areas (CSA) between chains or molecular objects.
Tested on Ubuntu Linux
mkdir dr_sasa cd dr_sasa git clone https://github.com/nioroso-x3/dr_sasa_n.git cd dr_sasa_n/ mkdir build cd build/ cmake ../ make cd .. cd .. pip install git+https://github.com/crosvera/contactplot.git
wget https://files.rcsb.org/view/2W26.pdb dr_sasa_n/build/dr_sasa -m 1 -i 2W26.pdb contactplot.py protein-ligand 2W26.LIGAND_vs_PROTEIN.by_atom.tsv 2W26.atmasa --skip-non-contact
Judemir Ribeiro, Carlos Ríos-Vera, Francisco Melo, and Andreas Schüller
Licensed under the terms of the MIT license. Copyright (c) 2018 Judemir Ribeiro, Carlos Ríos-Vera, Francisco Melo, and Andreas Schüller
J. Ribeiro, C. Ríos-Vera, F. Melo, and A. Schüller (2019), Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions. Bioinformatics, 35 (18), 3499-3501. https://doi.org/10.1093/bioinformatics/btz062.