Depends on the the kind of docking. If you have only few ligands, basic visualizing software like PyMol will do. If you are interested rather in virtual screening and docking of hundreds or thousands of ligands, I would reccomend Raccoon 2, which is included in the newest realease of AutoDock Tools. See http://autodock.scripps.edu/resources/raccoon2.
However, it is supposed your docking was made using AutoDock Vina.
Basic features: ligand clustering according to coordinates, distribution of binding energy values, calculation of ligand efficiency. You can also choose ligand-protein interactions to specific residues of your target to be preffered.
Hello
CASTp, Autodock vina, Swissmodel, Qsite, Chimera, RasMol or JMOL, MOE, BIOVIA Discovery Studio.
Good Luck.
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