So the AI agent that tried to publicly shame one of the matplotlib maintainers for closing his PR happens to also open PRs in rdkit, openbabel, pyscf, and other compchem libraries... Oh dear
Mols2grid 2.2.0 is out with full Marimo support 🎅 Huge thanks to @n283t.bsky.social for the contribution! See this for an example linking mols2grid selections with marimo's UI table: github.com/cbouy/mols2g...
N283T: x.com/tbsng_ktkm0923
User Webinar: Improving Pose Prediction Models for Drug Discovery. Join us for an insightful webinar with David Errington and Cedric Bouysset from Recursion, the authors of a recent study that challenges the current benchmarks in protein-ligand pose prediction.
David Errington and Cédric Bouysset @recursionpharma.bsky.social recently published a study that challenges the current benchmarks in protein–ligand pose prediction.
Register for the upcoming webinar to learn more: attendee.gotowebinar.com/register/599...
⌛9th Sept - 15:00 (BST)
#DrugDiscovery
"Celebrities turning 40 this week"
We believe that incorporating interaction-aware metrics into evaluation pipelines is essential for advancing the field, particularly for drug discovery applications. This could involve developing PLIF or pharmacophore-sensitive loss functions for training new ML models.
- While cofolding models show promise in predicting the full complex structure, our findings suggest a significant need for improvement in ensuring the predicted poses form meaningful interactions with the target protein.
- Our study shows that classical docking algorithms, when benchmarked with proper structure preparation, generally outperform current machine learning-based methods in recovering interactions.
- We introduce the Protein-Ligand Interaction Fingerprint (PLIF) recovery as an additional metric to directly assess the recall of these vital interactions.
Key takeaways:
- Focusing solely on ligand placement accuracy can overestimate model performance. We found that many predicted poses, especially from recent protein-ligand cofolding models, fail to capture key interactions.
We explore a critical aspect often overlooked in recent protein-ligand pose prediction benchmarks: the accurate recapitulation of protein-ligand interactions. While low RMSD and physical plausibility are important, they don’t tell the whole story.
Our work “Assessing interaction recovery of predicted protein-ligand poses” with David Errington, @cschneider.bsky.social and @fdreyer.bsky.social, previously presented at NeurIPS, is now published in the Journal of Cheminformatics! 🎉
Check out the full paper here: rdcu.be/emKgd
MDAnalysis UGM logo
#mdaUGM2025 is officially happening! Abstracts and travel bursary applications are being accepted from now until the July 15, 2025 deadline: www.mdanalysis.org/2025/04/13/u....
🗓️ November 9-11, 2025
📍Tempe, Arizona, USA (and online)
#open-source-software #molecular #simulations #streaming
Photo of the inside of a university building at WUR, it looks like a mix of a greenhouse with offices that have balconies.
We're offering a fully funded PhD at the intersection of ML/AI and the natural sciences with a focus on sustainability and chemistry.
You'll work at WUR in the Netherlands, ranked #3 in environ. sciences, #1 in agricultural science, #38 in life sciences (QS).
Apply here:
www.wur.nl/nl/vacature/...
Happy to share that I'll be once again mentoring Google Summer of Code applicants with MDAnalysis 🤠 This year, alongside pure-MDAnalysis projects, we have collaborative projects on MolecularNodes, WESTPA... and 3 projects ideas for ProLIF ✨ More info in the post below 👇
Here's a first:
I'm hiring a PhD student.
If you have (or know someone who has) a strong background and interest in computational (bio)chemistry or computer science (especially 3D computer vision), let's work together 😊
www.wur.nl/nl/vacature/...
var(){ _var=$(echo "$@" | perl -pe 's/(.+?) *= *(.+)/\1=\2/') && declare -g $_var;}
It's annoying that the `declare` command doesn't work like `set` in csh which allows `set var = value`, but with a little bit of dubious trickery:
"He's a little confused, but he's got the spirit"
