The thread below is to track the planning of both docking and free energy calculation simulations.
As a starting point, @JohnChodera has put up a github repo showing the preparation of docked structures.
I know @RGlen and Mark Williamson also have a repository that is worth sharing.
And I know Matt Hurley has started some free energy calculations.
That’s a great initiative!
Two questions:
Is there a central place where we should upload the docked poses/complexes, or will all ligands be docked (redocked)? (-or can we just push them to the github?)
What kind of methodology will be applied to score the complexes? i.e. I can imagine for closely related molecules relative free energy simulations make a lot of sense while for diverse molecules this is perhaps less the case.
Thanks,
Good question. What do you think @JohnChodera, a Github? I believe all ligands will eventually be redocked by at least one group, but might be good to compare to that of the submitter.
On this, I’ll refer to @JohnChodera and @RGlen, who are helping lead those efforts.