Download dr_sasa
Introduction
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.
Operation modes
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.
Downloads
Releases - Binary releases for Linux, MacOS and Windows, as well as the source code, are freely available from the GitHub repository
README - Usage instructions
INSTALL - Installation instructions
Contactplot - Python source code and installation instructions of the contactplot.py script to generate attractive 2D surface-based contact plots.
Installation instructions from source
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 ../..
pip install git+https://github.com/crosvera/contactplot.git
Test run
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
Authors
Judemir Ribeiro, Carlos Ríos-Vera, Francisco Melo, and Andreas Schüller
Contact: aschueller@bio.puc.cl
Licensed under the terms of the MIT license. Copyright (c) 2018 Judemir Ribeiro, Carlos Ríos-Vera, Francisco Melo, and Andreas Schüller
How to cite
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.