Peter Škrinjar
@peterskrinjar.bsky.social
PhD student at @biozentrum.bsky.social. I prefer protein interactions to human ones.
Reposted by Peter Škrinjar
🧪🧬🔬 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
www.biozentrum.unibas.ch/open-positio...
The position is initially funded for 3 years, possibility to start immediately.
#StructurePrediction, #Bioinformatics, #Uniprot3D, #AI
February 26, 2025 at 11:01 AM
🧪🧬🔬 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
www.biozentrum.unibas.ch/open-positio...
The position is initially funded for 3 years, possibility to start immediately.
#StructurePrediction, #Bioinformatics, #Uniprot3D, #AI
In case you missed it!
Thanks to everyone who joined us last week! You can now watch the recording of the webinar: youtu.be/_ykP_tEVrOk
February 24, 2025 at 4:42 PM
In case you missed it!
Reposted by Peter Škrinjar
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)
“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)
Redirecting
doi.org
February 21, 2025 at 5:13 PM
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)
“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)
Reposted by Peter Škrinjar
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.
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...
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...
February 20, 2025 at 12:34 PM
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.
Reposted by Peter Škrinjar
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...
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...
February 13, 2025 at 10:41 AM
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...
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...
Reposted by Peter Škrinjar
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...
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...
February 13, 2025 at 3:37 PM
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...
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...
Reposted by Peter Škrinjar
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)
(1/n)
February 10, 2025 at 1:28 PM
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)
(1/n)
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!
February 11, 2025 at 5:25 PM
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!
Reposted by Peter Škrinjar
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...
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...
February 10, 2025 at 1:43 PM
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...
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...
Reposted by Peter Škrinjar
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
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
February 8, 2025 at 1:35 PM
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
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
Reposted by Peter Škrinjar
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… ⬇️⬇️⬇️
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)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
Have protein-ligand co-folding methods moved beyond memorisation?
Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...
www.biorxiv.org
February 8, 2025 at 10:53 AM
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… ⬇️⬇️⬇️
Reposted by Peter Škrinjar
Basically, novelty is not defined by time in the PDB.
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)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
Have protein-ligand co-folding methods moved beyond memorisation?
Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...
www.biorxiv.org
February 8, 2025 at 10:38 AM
Basically, novelty is not defined by time in the PDB.
Reposted by Peter Škrinjar
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!
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)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
Have protein-ligand co-folding methods moved beyond memorisation?
Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...
www.biorxiv.org
February 8, 2025 at 10:30 AM
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!
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)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
Have protein-ligand co-folding methods moved beyond memorisation?
Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...
www.biorxiv.org
February 8, 2025 at 10:02 AM
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)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
Reposted by Peter Škrinjar
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
leaderboard & instructions are on mlsb.io
December 9, 2024 at 4:15 PM
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
leaderboard & instructions are on mlsb.io
Reposted by Peter Škrinjar
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
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....
onlinelibrary.wiley.com
December 9, 2024 at 8:31 PM
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
Reposted by Peter Škrinjar
AF3 BEST METHOD followed by cluspro but also some conversion errors
December 3, 2024 at 5:07 PM
AF3 BEST METHOD followed by cluspro but also some conversion errors
Reposted by Peter Škrinjar
@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.
December 3, 2024 at 5:17 PM
@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.
Reposted by Peter Škrinjar
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...
snf.ch/en/xgVKfkp88...
Torsten Schwede appointed as new President of the SNSF Research Council from 2025
Swiss National Science Foundation (SNSF)
snf.ch
December 8, 2023 at 12:20 PM
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...
snf.ch/en/xgVKfkp88...