suggesting Meeko to accurately convert PDBQT/DLG to SDF

[diogomart]

Hello,

Thank you for this great article.

I'd like to suggest Meeko to create PDBQT files for both AutoDock-GPU and Vina, and for exporting the docking results back to SDF. It writes a SMILES string in the PDBQT remarks and uses it to create an RDKit molecule with correct bond orders and formal charges. It also makes macrocyclic rings flexible.

https://github.com/forlilab/meeko
https://meeko.readthedocs.io

[Foly93]

Hi diogomart,

Thank you very much for your kind words and for sharing this suggestion — Meeko looks really interesting! I agree this could be a valuable addition.

At the moment I won’t be able to implement it right away, but I’ve added it to the to-do list for the next release and will at least test it out in the meantime.

Thanks again for the idea!

Best regards,

Luis

[diogomart]

Thank you for considering it! We just got a preprint out on Meeko: https://chemrxiv.org/engage/chemrxiv/article-details/68c054243e708a7649fa21d3