Ethan Holleman

Posts with the tag PyMOL:

Visualizing ligand docking results with PyMOL scripting and R

The past couple days I have been running some ligand docking simulations as part of my current rotation with the Cortopasssi lab using Rosetta. One of these docking simulations involved fitting a small portion of the insulin receptor (IR) the lab is interested in, into a known binding region of the Shc1 protein. Any Rosetta docking simulation will require hundreds of repetitions, which generate a significant number of pdb files which show the final conformation of the protein and ligand at the end of a given simulation. While reading about the best way to aggregate and do analyise on these results I spent a bit of time looking for ways to visualize everything Rosetta spits out.