F1000Research/ABS-Scan
Creators
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 PymolFiles
ABS-Scan-V1.0.zip
Files
(2.3 MB)
Name | Size | Download all |
---|---|---|
md5:c6aa87c95e68b3424c4ed1ca13159947
|
2.3 MB | Preview Download |
Additional details
Related works
- Is supplement to
- https://github.com/F1000Research/ABS-Scan/tree/V1.0 (URL)