ABS-Scan: F1000Research/ABS-Scan
praveeniisc · Zenodo (CERN European Organization for Nuclear Research) · 2014
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