2. Protein and ligand preparation and docking | AutoDock vina docking with Zinc metalloproteins скачать в хорошем качестве

2. Protein and ligand preparation and docking | AutoDock vina docking with Zinc metalloproteins

In this tutorial, we prepare zinc metalloprotein, prepare the ligand, and perform docking. We walk through the tutorial provided by AutoDock: https://autodock-vina.readthedocs.io/... Terminal commands: ---------------------------------- python2 prepare_receptor4.py -r protein.pdb -o protein.pdbqt python2 zinc_pseudo.py -r protein.pdbqt -o protein_tz.pdbqt conda activate vina mk_prepare_ligand.py -i ligand.sdf -o ligand.pdbqt --pH 7.4 cp ~/Downloads/AutoDock-Vina/example/docking_with_zinc_metalloproteins/data/AD4Zn.dat . python2 prepare_gpf4zn.py -l ligand.pdbqt -r protein_tz.pdbqt -o protein_tz.gpf -p npts=x,y,z -p gridcenter=x,y,z –p parameter_file=AD4Zn.dat ./autogrid4 -p protein_tz.gpf ./vina --ligand ligand.pdbqt --maps protein_tz --scoring ad4 --out docked.pdbqt --------------------------------------------------------------------------------------------------------------------------------------------------------------- LinkedIn:   / muhammad-i-ismail   GitHub: https://github.com/MuhammadIIsmail Research Gate: https://www.researchgate.net/profile/...