rdkbio.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Registration is open until March 6th!!

submitted 2 hours ago • 0 comments

🧪🧬🔬 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 1 day ago • 1 comment

🚨 Unravel BILLIONS of years of protein evolution! 🚨 How did protein structures emerge and evolve over deep time? Join @zachary-ardern in the next ProSE Seminar! 📅 March 11, 3PM GMT 🔗 tinyurl.com/prose-seminar2 #ProteinEvolution #StructuralBiology

submitted 2 days ago • 0 comments

In case you missed it!

submitted 3 days ago • 0 comments

Spouštíme nový web! 🎉 📚 Na bsky.cz nyní najdete naši „wiki“ s vysvětlením základních pojmů, užitečnými návody a dalšími informacemi. Budeme rádi, když nám ji pomůžete rozšířit ✍️ 📊 Statistiky českých uživatelů nyní běží na subdoméně stats.bsky.cz

submitted 3 days ago • 8 comments

Injecting arbitrary experimental data into AlphaFold has been a missing feature. With high-throughput crystallography yielding 1000s of structures/year (@covid_moonshot) & cryoET making 😍 but low-res in situ models, it's also become a necessary one for scaling up structural biology. Hence ROCKET👇!

submitted 3 days ago • 2 comments

📰 Svou barvitou cestu k vědě popsal Tomáš Pluskal (@pluskal-lab.org) z našeho ústavu v nedávném obsáhlém rozhovoru pro Hospodářské noviny. Více na ► vikend.hn.cz/c1-67616740-... ⤵️ #ceskaveda

submitted 3 days ago • 0 comments

MassSpecGym - the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. @roman-bushuiev.bsky.social @anton-bushuiev.bsky.social @josef-sivic.bsky.social @pluskal-lab.org NeurIPS 2024 paper: arxiv.org/abs/2410.23326 #ChemSky #MassSpec #AI4Science

submitted 7 days ago • 1 comment

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 6 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 7 days ago • 0 comments

MassSpecGym - the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. @roman-bushuiev.bsky.social @anton-bushuiev.bsky.social @josef-sivic.bsky.social @pluskal-lab.org NeurIPS 2024 paper: arxiv.org/abs/2410.23326 #ChemSky #MassSpec #AI4Science

submitted 7 days ago • 1 comment

Recent protein backbone design methods don't appear to uniformly improve upon pre-DL methods. This was evidenced by RFDiffusion's failure at motif scaffolding of two proteins that were designed by earlier methods arxiv.org/abs/2502.12479

submitted 7 days ago • 1 comment

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 14 days ago • 1 comment

We will be hosting the first @mzmine.bsky.social Community Meeting at @iocbprague.bsky.social. Please register if you wish to learn about the latest developments in mzmine. More info: docs.google.com/document/d/1...

submitted 10 days ago • 0 comments

🧵 on our preprint: Zhang & Skolnick's TM score for comparing model of protein to experimental structures of same protein. The d_j are essentially the same as the aligned error in Alphafold. After any structure alignment, it's the displacement of model Calpha from experimental Calpha of residue j.

submitted 11 days ago • 4 comments

If you’re submitting to the @narjournal.bsky.social Web Server/Database issue and need to add PMC and DOI links to your #BibTeX as required—but the provided Perl script isn't working—I’ve created a small Python script to help you out! 🔗 github.com/davidhoksza/...

submitted 11 days ago • 0 comments

Important #AlphaFoldology thread about scoring intramolecular complexes in #AF2 and #AF3

submitted 11 days ago • 1 comment

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 19 days ago • 4 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 17 days ago • 1 comment

🤔

submitted 14 days ago • 0 comments

We live in the dumbest timeline.

submitted 14 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 17 days ago • 1 comment

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 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 19 days ago • 1 comment

Things are often obvious, but sometimes less so. It is true also for small things like ligand-binding sites. In this work, our @cusbg.bsky.social group presents a new dataset designed for cryptic-binding site predictons - happy, to be part of this: academic.oup.com/bioinformati...

submitted 22 days ago • 0 comments

Picard tip for 2025

submitted 21 days ago • 0 comments

Is there a list of mirrored US public databases to European ones or others, e.g. PubMed -> EuropePMC, GenBank -> ENA, RCSB -> PDBe, etc.? You know, just in case?

submitted 22 days ago • 3 comments

MassSpecGym is the largest publicly available collection of mass spectra data with 231K spectra for 29K unique molecular structures. 33% of the dataset was generated from newly measured, in-house data. 🛡️The dataset is now certified on Polaris! polarishub.io/datasets/rom... youtu.be/G8ZnVRm0ogc

submitted 34 days ago • 1 comment

🏆 Cenu #Neuron pro mladé vědce získal v neděli také Dr. Tomáš Pluskal z našeho ústavu. Více na ► www.uochb.cz/cs/novinky/6... ⤵️ #cenaneuron #iocb #iocbprague #uochb #akademievedcr

submitted 37 days ago • 0 comments