There is a .PDB strucrure (X-ray) of a ligand bound protein. It is known that the ligind binding leads to moderate conformational changes around the ligand-binding site. Is it possible to obtain the native, ligand free protein .PDB strucrure by any kind of simulations? MD? Which program(s) could be suggested?
Any MD program can do this. Remove the ligand and simulate for sufficiently long and the structure should adapt to the change. Of course, you need some way to quantify whether or not you've arrived at a true apo structure (distances or other data from experiments) and the approach relies on a high-quality force field.
Hi,
i'm agree with Justin Lemkul there, you should use molecular dynamic simulation to achieve the native structure.
Use MD after deleting the ligands manually from the .pdb file to get the nearly native structure. But sometimes we are required to use the ligand bound conformation of the protein for testing competitive inhibitors. In that case, you can skip the MD step.
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