does any have the tenderbutton/dylan stiles archive in one place? #chemsky #chemchat There's a lot mirrored on archive.org but it would be great to have it fast, searchable and ideally complete somewhere
F.P. Morgan
@ecfp.bsky.social
cheminformatics @ všcht prague https://molecular.beauty github.com/dehaenw
now with fixed stereochemistry, easy installation via pip and large validation (99.998% roundtrip success on chembl) github.com/dehaenw/blincs
GitHub - dehaenw/blincs: Breadth-first Line Notation for Chemical Structures
Breadth-first Line Notation for Chemical Structures - dehaenw/blincs
github.com
new preprint, enjoy filtering and generating molecules! chemrxiv.org/doi/full/10....
LACAN: Leveraging adjacent co-occurrence of atomic neighborhoods for molecular scoring and generation Authors | ChemRxiv
LACAN (Leveraging Adjacent Co-occurrence of Atomic Neighborhoods) is a bond-level statistical scoring function and filter based on adjacent atomic environment co-occurrence. When integrated into evolutionary search it enables chemically constrained ...
chemrxiv.org
sad to see the low success rates of MSCA this year, with many excellently rated projects not meeting the unusually high funding threshold. wonder if the big increase in applications is due to the decline of american science funding and prestige
literally no one asked, but I started a newsletter. it’s called "This Week In Cheminformatics" (very original, I know). First issue is out now. have a read and a very happy new year ! thisweekincheminformatics.substack.com/p/one #cheminformatics
using 1999bit fingerprints so fits in the <2000 ft tabpfn limit. feels dirty
![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"](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:vyc7btogzsuabjp5bmcgfdg5/bafkreibfz5stv4z7d5g2rijtx6kpj3jpi4yiov4qaryhxxfx4hzmuwa3mq)
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
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...
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.
github.com
Today's #RDKit blog post is a heartfelt plea for clearer communication. greglandrum.github.io/rdkit-blog/p...
Please stop saying “The Tanimoto similarity is” – RDKit blog
A simple tip to explain what you actually did
greglandrum.github.io
out now in JCIM pubs.acs.org/doi/10.1021/...
CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13
AbstractA 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-1...
pubs.acs.org
F.P. Morgan@ecfp.bsky.social · last yr.glad to be on the CACHE #2 preprint chemrxiv.org/engage/chemr...
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
RDKit UGM 2025 in Prague (at VŠCHT) !
Greg Landrum@greglandrum.bsky.social · last yr.Pre-registration for the 2025 #RDKit UGM, to be held from 10-12 September in Prague, is now open! The link is below. Note that registration is a two-step process this year; there's more information in the form itself. forms.gle/pu7ELeUwARFQ...
Baseline approaches in the @polarishub.io x ASAP discovery x OpenADMET challenge (in advance of next week's leaderboard...) molecular.beauty/blog/2025/03...
”Baseline approaches in the Polaris challenge”
Molecular property prediction has a serious bottleneck: data. Commonly used benchmark data have various problems as talked about at length elsewhere. One organization which is trying to tackle this pr...
molecular.beauty
glad to be on the CACHE #2 preprint chemrxiv.org/engage/chemr...
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...
chemrxiv.org
The "FedEx arrow" of cheminformatics is the arrow in the letter D in the RDKit logo...
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 .
8th Advanced in silico Drug Design workshop 2025 – Katedra fyzikální chemie
kfc.upol.cz
is there currently an active leaderboard (guacamol style) for molecular generators?
ironic that the thing that might save us from from the mirror germ apocalypse is gonna be an L-ala-L-ala mimic beta lactam
RIP to a giant chem-bla-ics.linkedchemistry.info/2024/12/08/r...
Richard L. Apodaca
If you are into openscience chemistry or chemistry blogging, then you probably heard of Rich Apodaca’s Depth-First blog. Rich started blogging in 2006 but this is not how I discovered his work origina...
chem-bla-ics.linkedchemistry.info
we (#1715) placed 5th in the #CACHE3 challenge! (a lot of hits, but penalized due to novelty) As a cheminformatician, I love to see successful near neighbor behavior. Congrats to all involved and congrats to the 7-deazapurine and pyrimido[4,5b]indole scaffold. cache-challenge.org/results-cach...
Results of Cache Challenge # 3 | CACHE
Accelerating the impact of AI-driven Drug Discovery
cache-challenge.org
saw a cool tanimoto synonym in a prez today called IOU (intersection over union)
Save the date: I'm happy to announce that the 2025 RDKit UGM will take place in Prague, Czechia from 10-12 September. The organizers are Martin Šícho and Daniel Svozil from the University of Chemistry and Technology in Prague. Registration details will follow early next year.
great to join this #atom centered local neighborhood. #chemsky #MyFirstSkeet