iiinova — where your digital self keeps evolving

Reposted by Jerome Eberhardt

ForliLab @forlilab.bsky.social · 18/09/2025

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.

142

Reposted by Jerome Eberhardt

CAMEO-3D @cameo3d.org · 28/04/2025

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

177

Reposted by Jerome Eberhardt

Torsten Schwede @torstenschwede.bsky.social · 26/02/2025

🧪🧬🔬 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

Open Postdoc Position at the schwede lab, Biozentrum Basel.

12018

Reposted by Jerome Eberhardt

Peter Škrinjar @peterskrinjar.bsky.social · 11/02/2025

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!

1205

Reposted by Jerome Eberhardt

Cas @caswognum.nl · 08/02/2025

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

194

Reposted by Jerome Eberhardt

Torsten Schwede @torstenschwede.bsky.social · 08/02/2025

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… ⬇️⬇️⬇️

0193

Reposted by Jerome Eberhardt

Peter Škrinjar @peterskrinjar.bsky.social · 08/02/2025

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

2141

Jerome Eberhardt @jeeberhardt.bsky.social · 08/02/2025

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

0113

Reposted by Jerome Eberhardt

Janani Durairaj (Jay) @ninjani.bsky.social · 08/02/2025

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!

02510

Reposted by Jerome Eberhardt

bioRxivpreprint @biorxivpreprint.bsky.social · 08/02/2025

Have protein-ligand co-folding methods moved beyond memorisation? www.biorxiv.org/content/10.1101/202…

011

Reposted by Jerome Eberhardt

Keri Backus @keribackus.bsky.social · 20/01/2025

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...

0213

Reposted by Jerome Eberhardt

Janani Durairaj (Jay) @ninjani.bsky.social · 24/12/2024

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

plinder.sh

Updates

03813

Reposted by Jerome Eberhardt

Janani Durairaj (Jay) @ninjani.bsky.social · 09/12/2024

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

onlinelibrary.wiley.com

Automated benchmarking of combined protein structure and ligand conformation prediction

The prediction of protein-ligand complexes (PLC), using both experimental and predicted structures, is an active and important area of research, underscored by the inclusion of the Protein-Ligand Int....

153

Reposted by Jerome Eberhardt

Gabriele Corso @gcorso.bsky.social · 08/12/2024

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...

linkedin.com

Response to Jain et al.

You may have seen a recent pre-print [1] from Jain et al. with strongly worded claims against the experimental results in our DiffDock paper [2].

075

Reposted by Jerome Eberhardt

Janani Durairaj (Jay) @ninjani.bsky.social · 03/12/2024

@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.

083

Reposted by Jerome Eberhardt

Torsten Schwede @torstenschwede.bsky.social · 24/11/2023

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...

Cover of the special CASP issue in Proteins

0179