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Published August 26, 2014 | Version V1.0
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F1000Research/ABS-Scan

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Description

ABS-Scan

Alanine binding site scanning mutagenesis for evaluting the contribution of individual residues at the binding site towards small-molecule ligand recognition. Web-server

We strongly recommend user-friendly webserver available at http://proline.biochem.iisc.ernet.in/abscan

Graphical output provided on webserver:

Example output can be visualized by clicking here - Examples Command-line usage

./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. Dependencies

Please ensure following are installed on your system:

Modeller MGL autodockTools Pymol

Files

ABS-Scan-V1.0.zip

Files (2.3 MB)

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