Alanine binding site scanning mutagenesis for evaluting the contribution of individual residues at the binding site towards small-molecule ligand recognition.
We strongly recommend user-friendly webserver available at http://proline.biochem.iisc.ernet.in/abscan
Graphical output provided on webserver:
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Example output can be visualized by clicking here - Examples
./alanine_scanning.py -h
usage: alanine_scanning.py [-h] [-f PDBFILE] [-n RESNO] [-d DIST] [-o OUTDIR]
Arguments:-h, --help show this help message and exit
-f PDBFILE PDB file of protein-ligand complex
-n RESNO residue number of HETATM in protein-ligand complex
-d DIST distane-cutoff to use for defining the binding site
-o OUTDIR output directory to store the results
Ex:./alanine_scanning.py -f 1a4g_A.pdb -n 466 -d 4.5 -o ./test
In the above example :
1a4g_A.pdb -- It is the PDB file containing the protein-ligand complex.
466 -- is the residue ID for the ligand - ZMR
4.5 -- is the distance cut-off used to select the binding site residues from mentioned ligand atom
test -- is the directory that would be created to store the results.
Please ensure following are installed on your system: