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aspuru-guzik-group / selfies

Robust representation of semantically constrained graphs, in particular for molecules in chemistry
Apache License 2.0
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Nano particle selfies #95

Closed jessielyons closed 1 year ago

jessielyons commented 1 year ago

Dear authors,

Can you please guide me if I can use SELFIES for nano particles? Also how does SELFIES relate to quasi-Smiles representation?

Any guidance will be really helpful. Thanks so much!

Cheers, Jessie

MarioKrenn6240 commented 1 year ago

I cannot help there and i have not heart of quasi-smiles representation, but maybe @whitead can jump in?

whitead commented 1 year ago

Quasi-SMILES looks a lot like CXSMILES. You can take a look a that, which is supported in standard tools like rdkit.

Not sure what your goal is, but you can represent the nanoparticle with something like [Au] and set-up a rule for its valence. However, SELFIES only captures atoms/bonds. If you have other properties, you should consider a different representation.

whitead commented 1 year ago

A recent paper on SMILES for composite compounds like nanoparticles: https://pubs.acs.org/doi/10.1021/acs.jcim.2c00690

jessielyons commented 1 year ago

Hi all, thank you for your responses. Sorry I didn't clarify that I am only interested in lipid nanoparticles and siRNA.

  1. First, how do you suggest we can use SELFIS especially for lipid nanoparticles?
  2. Second, can all SMILES extracted from Drug Bank be converted into SELFIS?
  3. Do you recommend if selfis can be used for siRNA for which "canonical smiles" are available?

I am asking these questions as based on my review of your publications and lectures. I understood that all smiles can be converted into selfis and that selfis is much better representation than smiles. Apologies for all the confusion I may have created.

Thanks again, Jessie