Output autobox results

[Goran Rakocevic]

Is it possible to extract the search space which was defined by the autobox procedure? Perhaps the info is there, but I'm just missing it.

I'd like to distribute across several processes, while using autobox up front (and then passing in the values as coordinates). Also, sometimes it's good to know what the box was, when inspecting the results.

Thanks!
Goran

[David Koes]

There isn't any option to print this out, but you can calculate it yourself. Take the max/min x/y/z value of the autobox_ligand coordinates and add/subtract autobox_add.

[Yuning Shen]

Hi, David. What would happen if ligands are located at different (possibly distant) binding sites? Will it generate a too large box containing all the ligand atoms?

Thanks!
Yuning

[David Koes]

Yes. For example, you can do whole protein docking by passing the receptor as the autobox_ligand.

[Yuning Shen]

Thanks for the fast reply! Is it recommended (efficient) to dock small molecules to the whole protein? Do we need to adjust other parameters accordingly (e.g. large exhaustiveness for sufficient exploration of a large space)?

[David Koes]

You generally only do whole protein docking when you don't know the binding site. It is not recommended if you know the binding site. You definitely want to substantially increase the exhaustiveness when doing whole protein docking (how much depends on the size of the protein).

[Yuning Shen]

Thank you for the explanation!