🦠 Model Request: PGMG pharmacophore-based generative model

[miquelduranfrigola]

Model Name

Pharmacophore-guided molecular generation

Model Description

Based on a molecule's pharmacophore, this model generates new molecules de-novo to match the pharmacophore. A graph neural network encode spatially distributed chemical features and a transformer decoder generates molecules

Slug

pgmg

Tag

Compound generation

Publication

https://www.nature.com/articles/s41467-023-41454-9

Source Code

https://github.com/CSUBioGroup/PGMG

License

GPLv3

[miquelduranfrigola]

A critical point here is the generation of pharmacophores given a SMILES molecule. This needs to be done automatically.

For context, see this issue: https://github.com/CSUBioGroup/PGMG/issues/7

[miquelduranfrigola]

/approve

[github-actions[bot]]

New Model Repository Created! 🎉

@miquelduranfrigola ersilia model respository has been successfully created and is available at:

🔗 ersilia-os/eos69e6

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[miquelduranfrigola]

See discussion on authors repository about generating pharmacophore files: https://github.com/CSUBioGroup/PGMG/issues/7 Interestingly, they also offer a web server: https://www.csuligroup.com/PGMG/#/submit

[GemmaTuron]

@miquelduranfrigola we have been having the pgmg model hanging around for a while. We are well covered now in generative models I think, specially with the summer sprint. Do we close it and do not incorporate it or we do and finish this issue?

[miquelduranfrigola]

I would like to finish this. This model is important for scaffold hopping so, whenever we retake ChemSampler, it can prove to be useful. We just need to decide when we allocate the time.