F.P. Morgan

A black hat with an illustration of the transition state of the 6+4 cycloaddition between tropone and dimethylfulvene, and a black beanie that reads "55 years of the [6 + 4] reaction"

need this custom hat i found on the Ken Houk group website #chemsky

pubs.acs.org/doi/10.1021/...

CADD milestone for me: glad to have our first compounds in the PDB (virtual screened by our team during CACHE#3) : 7HQH, 7HQM, 7HQL, 7HQE, 7HPL, 7HPS, 7HQ5, 7HQO, 7HQP, 7HPY, 7HPX, 7HQ8

GitHub - wolberlab/OpenMMDL: Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes - wolberlab/OpenMMDL

haven't tried it myself, but saw a presentation on this one by @talagayev.bsky.social and it looked good github.com/wolberlab/Op...

openmm is great for this purpose, good python bindings and easy installation (for md standards...)

that's not the SMILES of oxalic acid, and the structure shown also isn't oxalic acid nor carbonate.

GitHub - dehaenw/ultra_enumerate: enumerate a large amount of rdkit valid SMILES. enumerate a large amount of rdkit valid SMILES. Contribute to dehaenw/ultra_enumerate development by creating an account on GitHub.

sometimes, you simply require thousands of unique SMILES for the same molecule (e.g. teaching a language model to pretend it's a graph based model instead). A prototype of the trivial "solution" to this problem using disconnected atoms dialect of SMILES is here now: github.com/dehaenw/ultr...

Paraquat might be unstable upon pyrolysis. Turns to less toxic bipyridine apparently. Upon looking it up, toxicity to dopaminergic neurons of paraquat has been extensively studied and was shown to be real, so while I can't speak for the real PD risk, the biological proof-of-concept is there

it seems obvious it could cause PD, given its similarity to MPP+

yes, me. i used marvinsketch for some time because it was linux friendly

GitHub - HaolinZhan/PE-NMR Contribute to HaolinZhan/PE-NMR development by creating an account on GitHub.

github.com/HaolinZhan/P... (agree that it's weird it's not linked by the journal, and not claiming a few example matlab files are satisfactory)

Today's #RDKit blog post is a heartfelt plea for clearer communication.
greglandrum.github.io/rdkit-blog/p...

out now in JCIM pubs.acs.org/doi/10.1021/...

Professor Taffee Tanimoto in class with his students at the former Park Square campus, circa 1966

A rare pic of Taffee Tanimoto (of Tanimoto similarity fame) in front of the classroom ca 1966. Source: web.archive.org/web/20040906...

One for the #Alphafoldogy lovers: Reproducible severe ligand hallucination that commonly occurs in AF3-likes: cyclohexane to benzene
Boltz (1.0.0) input
>A|smiles
C1CCCCC1CCN(C1CCCCC1)CC1CCCCC1
output in the pic below

just sneakily registered for the #ICCS2025 , looking forward to impressing everyone except dutch people by impeccably pronouncing noordwijkerhout in verkavelingsvlaams

it's a "cautionary principle" model - assumes every unseen chemical is toxic just to be sure!

RDKit UGM 2025 in Prague (at VŠCHT) !

Baseline approaches in the @polarishub.io x ASAP discovery x OpenADMET challenge (in advance of next week's leaderboard...) molecular.beauty/blog/2025/03...

nice, as the product is a michael acceptor too it might even be possible to conjugate with a second AA...

Hyperzrone A: great structure and great name to boot

CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13 A critical assessment of computational hit finding experiments (CACHE) challenge was conducted to predict ligands for the SARS-CoV-2 Nsp13 helicase RNA binding site, a highly conserved COVID-19 target...

glad to be on the CACHE #2 preprint chemrxiv.org/engage/chemr...

The activity of this new compound is unknown, but Taxol itself has low oral bioavailability and is actually not that potent, being dosed at 100-175 mg/m2 IV. Seems like it wouldn't be that difficult to safely deal with in an academic lab.

Chemical space(s) molecular.beauty/blog/2025/03...

The "FedEx arrow" of cheminformatics is the arrow in the letter D in the RDKit logo...

TGIBF₃

submitting something tonight!

Tomorrow starts the 8th Advanced in Silico Drug Design Workshop #8ADD
www.kfc.upol.cz/8add
organized by Pavel Polishchuk from IMTM LF UP, me from @fchupol.bsky.social, our colleagues, and students and supported by @elixircz.bsky.social .

theres an interesting parallel on a quite fundamental level too, in the microsound area the gabor wavelet made the wave particle duality and time-freq uncertainty principle directly relevant for sound synthesis

see the original claim here, it's a bit more clear particularly when shown superimposed on the 3d structure x.com/btnaughton/s...