New ligands docking

[PARODBE]

Hi!

Congrats for this amazing library!. Imagine, that you have created a generative model for ligand generation and you have 30-40 new ligands which aren't include in pdb obviously. Could you provide code or and example doing docking without using pdb? You could some random smiles as an example, is not necessary include the generative model. Also, it would be interesting generate the docking for a set of smiles instead of only one smile.

Thanks!

[AndreaVolkamer]

@PARODBE thanks for the positive feedback.
I'm not 100% sure if I understand your question correctly. Setting the generative modelling part aside (for which we do not provide talktorials yet), T015 and T018 (the latter still lives in PR 125, but will be merged soon) exemplify how to dock molecules starting from a SMILES string only. T015 shows the process for a single molecule from SMILES (see smiles_to_pdbqt function), T018 contains functions to process a set of molecules represented as SMILES (see __init__in docking class using an openbabel-based helper function obabel.create_pdbqt_from_smiles).

[PARODBE]

Thanks!, may be another option could be using mda, I have built it in this way:

And after we can follow your code of run_smina.

By the way, when you select the pocket size and pocket center:
pocket_center = (ligand.positions.max(axis=0) + ligand.positions.min(axis=0)) / 2
pocket_size =ligand.positions.max(axis=0) - ligand.positions.min(axis=0) + 5

I understand that the reason of sum 5 to pocket size is for cover more space or possibilities, or may be not? and in pocket_center the division /2??

Thanks for all!

Pablo

[AndreaVolkamer]

Thanks for the mda code snippet!

Regarding the pocket center questions:

• the pocket center is positioned half way between the two extrem values of the ligand atoms' coordinates, e.g. the max-min/2
• and yes, the pocket size is enlarged by 5 to be able to sample the space around the bound ligand more exhaustively (5A or sth in that range is often chosen, though still an arbitrary number)