#toolsperweek #structurebioinformatics #surfaceracer #loopsandstrands #protocols

Surface Racer calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules. The program also analyzes cavities in the protein interior inaccessible to solvent from outside. The output includes the surface parameters for each residue in addition to those for individual atoms.

This software could be an option to validate protein-protein docking where the docking poses can be filtered based on the least surface area between two protein chains/objects

LOOPS & STRANDS - Bioinformatics Protocols www.llbschool.org/magazine

@letslearnbioinformatics

#toolsperweek #structurebioinformatics #surfaceracer #loopsandstrands #protocols

Estimating the Solvent Accessible Surface Area of a Protein-Protein Complex

SOURCE:
https://tsodikovlab.createuky.net/index_files/Surface_Racer.htm

INSTALLATION:
1. Download it from here https://tsodikovlab.createuky.net/index_files/Surface_Racer.htm
2. Extract the downloaded file
3. Place all the input structures under the extracted directory name 'SURFACE_RACER_5_0'
4. Execute the below command

COMMAND:
./surface_Racer a input.pdb r m

-a Van del Waals radii sets
(you can choose either 1 - Richards (1977) or 2 - Chothia (1976)

Input.pdb

r Input the probe radius in Angstroms
(which is usually 1.4)

m Enter a number to choose the calculation mode
This can be either one below
1- Accessible surface area only
2- Accessible and molecular surface areas
3- Accessible, molecular surface areas and average curvature of MS

You get the output in result.txt where you can find the Molecular Surface Area (MSA)

Stay tuned for more Bioinformatics protocols
LOOPS & STRANDS: www.llbschool.org/magazine

@letslearnbioinformatics