Topic automatically created for discussing the designs at:
https://covid.postera.ai/covid/submissions/1a381570-5caa-4095-b2ba-625dc8939023
Hi!
I am one of the primary researchers (Andrew Brereton) who developed these molecules, in conjunction with Vijay and the rest of the Cyclica team! If anyone has any questions feel free to ask, we’re happy to clarify!
Hopefully it helps that the molecules should all be already in the Enamine REAL space, this is something we really wanted to focus on at least for first steps.
Big thanks to the PostEra team and all involved, this is an amazing effort! Can’t wait to see results starting to come!
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Hi, thank you for your detailed entry and hard work on this project!
So I just did some analysis on the synthesis of all of the compounds and noticed that only one of these seems to be directly in REAL space (VIJ-CYC-1a3-11). However, from your post, it seems that you wanted all of them to be in REAL space. Are you perhaps using an old version of the database?
Thanks,
Matt
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That may be possible 
Are you using the REAL space navigator from BioSolveIT? Or searching in the “available for purchase” REAL space?
Additionally, if it might help, we could privately (with Enamine’s blessing) share the synthons and reaction for each molecule individually! That might cover any non-exact smiles string matches that may be attributed to canonicalization / sanitizations.
Thanks,
Andrew
Hmmmm.
So are these different? I haven’t used the REAL Space Navigator from BioSolveIT, but do you have to update it as things go in and out of stock? I am querying the database directly in my code.
And sure, definitely feel free to email me at matthew.robinson@postera.ai if that helps. I have easy syntheses (high probability and 1-3 step) for a few of your compounds from Enamine BBs, but might help me double check availability / canonicalization issues if you send over your proposed building blocks.
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So are these different? I haven’t used the REAL Space Navigator from BioSolveIT, but do you have to update it as things go in and out of stock? I am querying the database directly in my code.
My understanding is that Enamine has about 7 million REAL space molecules which are “off the shelf”, as in available for immediate purchase. The full REAL space is comprised of ~4 x 10^9 molecules, but they need to be syntehsized (which Enamine says will take ~30 days with an 80% success rate). So our software is designed to explore the larger space, and primarily produces the second type of molecule. Though it’s an added bonus if it ends up producing readily purchasable compounds as well!
And sure, definitely feel free to email me at matthew.robinson@postera.ai if that helps. I have easy syntheses (high probability and 1-3 step) for a few of your compounds from Enamine BBs, but might help me double check availability / canonicalization issues if you send over your proposed building blocks.
Great! Sending an email now!
Hi guys,
Enamine kept this a bit confusing, but theser are two different resources:
- the REAL Database which contains 1 billion molecules. This is a big smiles / sd file which can be used whatever search engine.
- the REAL Space, which is 13 billion molecules. This is only searchabel with BioSolveIT’s technology, as it is a so-called fragment space (consisting of building blocks and rules how to combine them).
Both are on-demand compounds and are synthesizes upon request. Both with an extraordinary high likelyhood of >80 %.
@mc-robinson if you need a license for the option 2, please email me 
Cheers,
Franca
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Ok, great thanks @Franca – that is confusing! . I may just email you quite soon. Is there a way to search BioSolveIT’s database by API/command line? There are now over 2000 molecules so a batch submission would be ideal.
Actually, I see you’ve already helped John Chodera with this, so I can ask him for instructions! Will email you for a license, thanks!