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peterskrinjar.bsky.social
PhD student at @biozentrum.bsky.social. I prefer protein interactions to human ones.
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🧪🧬🔬 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

submitted 3 days ago • 1 comment

In case you missed it!

submitted 4 days ago • 0 comments

Some very cool stuff from the group now in paper form: “ModelArchive: a deposition database for computational macromolecular structural models” doi.org/10.1016/j.jm... And “Comparing macromolecular complexes - a fully automated benchmarking suite” doi.org/10.21203/rs.... (under review)

submitted 7 days ago • 0 comments

Join us tomorrow to hear @peterskrinjar.bsky.social talk about 🌹 Runs N' Poses 🌹! Curious to hear your thoughts on how to keep up with benchmarking in this field.

submitted 9 days ago • 0 comments

RT please: Just 1.5 months away from our joint 3DBioinfo/3DSIG amazing conference! These are our two great keynote speakers! @rolanddunbrack.bsky.social & @silviaosuna.bsky.social! Check our preliminary programme here: www.iscb.org/3dbioinfo202... Registration link: www.iscb.org/3dbioinfo202...

submitted 16 days ago • 1 comment

We’re hosting @peterskrinjar.bsky.social for a webinar to discuss his latest paper “Have protein co-folding methods moved beyond memorization?”! Join live on Feb 21st at 11 AM ET. Register here: us06web.zoom.us/webinar/regi... Explore Runs N’ Poses on Polaris today: polarishub.io/benchmarks/p...

submitted 16 days ago • 0 comments

How long does it take to predict ligand binding sites for all 220k proteins in the PDB? P2Rank 2.5 does it in 3 hours on a single CPU (16-core amd 5950x)—2x faster than the previous version 🚀. (1/n)

submitted 19 days ago • 1 comment

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!

submitted 17 days ago • 1 comment

We’re extremely excited to host Runs N’ Poses on Polaris! The authors show how current co-folding methods struggle to generalize beyond ligand poses in their training data. Explore the benchmark: polarishub.io/benchmarks/p... Explore the dataset: polarishub.io/datasets/pli...

submitted 19 days ago • 0 comments

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

submitted 21 days ago • 1 comment

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… ⬇️⬇️⬇️

submitted 21 days ago • 0 comments

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

submitted 21 days ago • 0 comments

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!

submitted 21 days ago • 0 comments

Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹! www.biorxiv.org/content/10.1... 🧵👇 (1/n)

submitted 21 days ago • 4 comments

Re docking: @workshopmlsb.bsky.social has been piloting a leaderboard for the PLINDER benchmark. It would be awesome to get submissions using existing methods, then everyone can see comparisons better 😁 leaderboard & instructions are on mlsb.io

submitted 82 days ago • 1 comment

AF3 BEST METHOD followed by cluspro but also some conversion errors

submitted 87 days ago • 2 comments

@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.

submitted 87 days ago • 0 comments

It is a great privilege and honor to be elected as new President of the SNSF Research Council. I’m very much looking forward to serving the Swiss scientific community in this new role in the coming years. snf.ch/en/xgVKfkp88...

submitted 449 days ago • 0 comments