Excited to announce a preprint describing our software package Meeko! Meeko is a Python package that uses RDKit for receptor and ligand preparation, including protonation, bond order, and connectivity and processing of docking results. It is customizable and suitable for high-throughput workflows.

Introducing CAMEO Structures & Complexes - automated weekly blind benchmarking of structure prediction servers. Now with heteromeric and protein-ligand complexes.
Join us and register your server now!
cameo3d.org

🧪🧬🔬 Postdoc in Computational Structural Biology at the @biozentrum.unibas.ch & @sib.swiss in Basel, Switzerland.

www.biozentrum.unibas.ch/open-positio...

The position is initially funded for 3 years, possibility to start immediately.

#StructurePrediction, #Bioinformatics, #Uniprot3D, #AI

We re-ran AF3 without templates, since we noticed it could use any template in the PDB, including the ground truth. We see the performance drops slightly in the lowest bins, but the gap to other methods still exists. We will update the preprint shortly!

New leaderboard on @polarishub.io for Runs 'N Poses! 🎸

Anyone has any protein-ligand co-folding methods laying around they would like to put to the test?

polarishub.io/benchmarks/p...

Great work @peterskrinjar.bsky.social @jeeberhardt.bsky.social @torstenschwede.bsky.social @ninjani.bsky.social

Have #AI methods for protein-ligand co-folding moved beyond memorisation and predict really novel leads for #drugdiscovery? Or do we find “more of the same”? This new benchmark lets you find out… ⬇️⬇️⬇️

I want to thank my co-authors @jeeberhardt.bsky.social, @torstenschwede.bsky.social, @ninjani.bsky.social and all of our collaborators! RunsN’ Poses builds on PLINDER and OpenStructure—this work wouldn’t be possible without them!
Also thanks to @rokbreznikar.bsky.social for this amazing logo! 9/9

Basically, novelty is not defined by time in the PDB.

We’ve been benchmarking deep learning co-folding methods for protein-ligand complex prediction, leading to the creation of 🌹Runs N’ Poses🌹. Great effort by @peterskrinjar.bsky.social and @jeeberhardt.bsky.social putting this together so quickly. Please have a look, excited for community feedback!

Have protein-ligand co-folding methods moved beyond memorisation? https://www.biorxiv.org/content/10.1101/2025.02.03.636309v1

First lab #Chemrxiv preprint of 2025 and first foray into AI-based discovery of reactive cysteines! Congrats to First author Lisa Boatner and thanks to @forlilab.bsky.social, @jeeberhardt.bsky.social, and the rest of the team for the stellar collaboration! chemrxiv.org/engage/chemr...

Here's a year-end update from #PLINDER. It's been really great working on this project and all the other projects that it has kickstarted - the gift that keeps on giving.

Happy holidays everyone!

www.plinder.sh/blog/updates

We actually had a similar benchmark (with LDDT-PLI) in the same CASP15 issue a while ago (onlinelibrary.wiley.com/doi/10.1002/..., Fig3B) conclusions were (1) pocket detection needed for physics-based (2) DL models overfit (3) nothing performs on non "re-docking". Was my main inspiration for PLINDER

Hi @ddelalamo.bsky.social unfortunately, this paper from Jain et al. contains falsehoods, misleading comparisons, seemingly deliberate omissions, and is written in a tone not intended as a serious research paper. Please see our detailed response: www.linkedin.com/pulse/respon...

@jeeberhardt.bsky.social presenting CASP16 PLI baselines. Big shout out to @jeremywohlwend.bsky.social and @gcorso.bsky.social for helping us with running Boltz-1 on short notice! Pretty weird results on autotaxin.

The #CASP15 special issue has been published in PROTEINS. #OpenAccess

We want to thank all contributors to the CASP experiment and remind everyone that #CASP16 is only half a year away.

CASP organizers

onlinelibrary.wiley.com/toc/10970134...