Dear All,
I want to if there is any protocol available to simulate and analyze the entry of a drug to a binding pocket of a protein as well as binding at that position. All I could find is the dynamics of protein-ligand interaction.
Tool: Gromacs
You can do this brute force with normal unrestrained simulations (with the ligand starting in the solution rather than bound to the protein), but that's not practical because it can take an extremely long time (milliseconds or more, probably) before it binds to the real binding site. The other approach is to use the pull code to guide the ligand into the binding site, but that assumes you (1) know the binding site and (2) already have a rough idea of the binding pathway already.
You can do this brute force with normal unrestrained simulations (with the ligand starting in the solution rather than bound to the protein), but that's not practical because it can take an extremely long time (milliseconds or more, probably) before it binds to the real binding site. The other approach is to use the pull code to guide the ligand into the binding site, but that assumes you (1) know the binding site and (2) already have a rough idea of the binding pathway already.
You might also try metadynamics, see for instance
Provasi et al. http://pubs.acs.org/doi/abs/10.1021/bi901494n
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