How do I convert a database of 100000 molecules to 3d sructure?

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Ricardo J Ferreira

Hi,

I would recommend you to load it to DataWarror and generate the lowest energy conformer. It is one of the best ways to deal with so many molecules. Then you just have to convert them with OpenBabel without generating the 3D coordinates (alternatively you can use the .sdf if using gnina)

Ayesha Fatima

Thank you Ricardo.

I did use the datawarrior but the problem with babel is that it gives me errors of stereochemistry and gets stuck. so i cannot get the molecules.

i also tried using rdkit but somehow i get stuck with reading files.

thank you anyways

take care

Andrea Mauri

Hi Ayesha Fatima you can check alvaMolecule (https://www.alvascience.com/alvamolecule/). Is a tool for data curation and it is free for academic purposes. It cannot convert 2D structures in 3D structures but can help you in identifying and fixing possible issues in your dataset. You can check some introductory video at https://www.youtube.com/playlist?list=PL480TqS_5JUDRJbNugMViz12PeSnyBfmk