Author | Lightnews

Reposted by Janani Durairaj (Jay)

Mohammed AlQuraishi @moalquraishi.bsky.social · 7d

OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇

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Irina Bezsonova @irinabezsonova.bsky.social · Oct 3

This October I’m drawing one molecule a day inspired by proteins in pdb @rcsbpdb.bsky.social

Day 2/31
Prompt WEAVE

N-terminal domain of a Fibrion - a building block of silk fiber produced by silkworms.

Pdb: 3UA0

Next prompt is CROWN and I would love your suggestions!

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Roni Odai @rodai.bsky.social · Oct 2

Viral AlphaFold Database (VAD) is live in Science Advances

~27,000 predicted viral protein monomers & homodimers

Conserved folds across bacteria, archaea & eukaryotic viruses

New toxin–antitoxin system KreTA uncovered

Vast “functional darkness” remains uncharted

www.science.org/doi/10.1126/...

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes

VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.

www.science.org

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SIB Swiss Institute of Bioinformatics @sib.swiss · Sep 10

Océane Follonier @oceanef.bsky.social for
“From bytes to binders: design, score and optimize” #bc2basel #posterprize

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Torsten Schwede @torstenschwede.bsky.social · Aug 27

Critical benchmarking of structure prediction methods has been crucial for measuring progress and detecting breakthroughs. But how will the future look like? Join the discussion at our workshop in Basel on September 8 - just before the [BC]2 conference.

@sib.swiss @biozentrum.unibas.ch

⬇️⬇️⬇️

CAMEO-3D @cameo3d.org · Aug 27

🔬 Workshop: Future of Structure Prediction Benchmarking
📅 Sept 8, 2025 | Basel
💡 Talks + breakout sessions on #CASP #CAPRI #CAMEO & benchmarking for drug discovery
🎟️ Free registration (limited spots): lu.ma/ws9nu1xf
Join us to explore how benchmarking can drive breakthroughs in structure prediction.

The future of structure prediction benchmarking: measuring progress and breakthroughs · Luma

Benchmarking has been a key driver of progress in protein structure prediction methods. As the field continues to evolve, several key questions prevail: How…

lu.ma

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Reposted by Janani Durairaj (Jay)

Martin Pacesa @martinpacesa.bsky.social · Aug 27

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.

www.nature.com/articles/s41...

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Janani Durairaj (Jay) @ninjani.bsky.social · Aug 27

Still some spots left, join us in Basel on Sep 8 (before [BC]2) to discuss structure prediction benchmarking and more!

CAMEO-3D @cameo3d.org · Aug 27

🔬 Workshop: Future of Structure Prediction Benchmarking
📅 Sept 8, 2025 | Basel
💡 Talks + breakout sessions on #CASP #CAPRI #CAMEO & benchmarking for drug discovery
🎟️ Free registration (limited spots): lu.ma/ws9nu1xf
Join us to explore how benchmarking can drive breakthroughs in structure prediction.

The future of structure prediction benchmarking: measuring progress and breakthroughs · Luma

Benchmarking has been a key driver of progress in protein structure prediction methods. As the field continues to evolve, several key questions prevail: How…

lu.ma

1 2

Reposted by Janani Durairaj (Jay)

CAMEO-3D @cameo3d.org · Aug 27

🔬 Workshop: Future of Structure Prediction Benchmarking
📅 Sept 8, 2025 | Basel
💡 Talks + breakout sessions on #CASP #CAPRI #CAMEO & benchmarking for drug discovery
🎟️ Free registration (limited spots): lu.ma/ws9nu1xf
Join us to explore how benchmarking can drive breakthroughs in structure prediction.

The future of structure prediction benchmarking: measuring progress and breakthroughs · Luma

Benchmarking has been a key driver of progress in protein structure prediction methods. As the field continues to evolve, several key questions prevail: How…

lu.ma

1 4

Reposted by Janani Durairaj (Jay)

EMBL Events @events.embl.org · Jul 24

Join us at #EMBOComp3D to explore cutting-edge breakthroughs in computational structural biology, AI, drug design, and innovative software! 💻

Find out about molecular modelling to systems-level analyses and evolution, and more.

Submit your abstract by 26 Aug ➡️ s.embl.org/csb25-01-bl

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CATH-Gene3D @cathgene3d.bsky.social · Aug 22

CATH turns 30 years old this year!

We are organising a 1-day symposium on September 16th at UCL, highlighting recent AI-based developments to enhance protein family classifications, annotations and analyses.

www.eventbrite.co.uk/e/protein-an...

Protein Annotations in the age of AI

A not-for-profit symposium hosted at UCL - more details about speakers and venue below.

www.eventbrite.co.uk

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Kieran Didi @kdidi.bsky.social · Aug 15

AtomWorks is out! Building upon @biotite_python, we built a toolkit for all things biomolecules and trained RF3 with it. All open-source, test it via `pip install atomworks`!

AtomWorks: github.com/RosettaCommo...
RF3: github.com/RosettaCommo...
Paper: tinyurl.com/y2w4z65b

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CAMEO-3D @cameo3d.org · Aug 8

Filtering out homologous structures from the PDB at 40% sequence identity is not enough to create a robust test set. Significant leakage persists at this level, and comparative modeling can still produce high quality models.

Scatter plot of LDDT as a function of sequence identity for high coverage homology models. The horizontal red line at 40% sequence identity highlights the presence high quality models in the low sequence identity region.

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Torsten Schwede @torstenschwede.bsky.social · Aug 7

Looking for a #fellowship for an independent #PhD at one of the best places for life sciences in the world?

The summer call at @biozentrum.unibas.ch @unibas.ch is open until October 12, 2025.

www.biozentrum.unibas.ch/phd/internat...

Biozentrum PhD Fellowships

Share your passion for life sciences. If you are talented and highly motivated, want to broaden your horizons and are interested in a wide range of research topics, apply for one of the sought after B...

www.biozentrum.unibas.ch

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Yo Akiyama @yoakiyama.bsky.social · Aug 5

Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

Scaling down protein language modeling with MSA Pairformer

Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...

biorxiv.org

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Sergey Ovchinnikov @sokrypton.org · Aug 5

The big difference is in the pairing. The MMseqs2 server pairs sequences based on species, while our old HHblits MSAs were paired based on genome proximity (number of genes apart). Working w/ @milot.bsky.social and @martinsteinegger.bsky.social we implemented the proximity filtering in server (3/4)

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Martin Pacesa @martinpacesa.bsky.social · Jul 25

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

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Pat Walters @wpwalters.bsky.social · Jul 22

New Practical Cheminformatics Post
patwalters.github.io/Three-Papers...

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Torsten Schwede @torstenschwede.bsky.social · Jul 5

We will be hosting a mirror site of the CASP data and workflows at @sib.swiss. Operating a redundant site with independent funding is a good idea for important scientific infrastructure, independent from the current funding situation in the US.

Max Fürst @maxfus.bsky.social · Jul 4

Guess a natural fit to take over would be @embl.org @ebi.embl.org @ewanbirney.bsky.social

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Jason Nomburg @jnoms.bsky.social · Jun 12

Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!

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SIB Swiss Institute of Bioinformatics @sib.swiss · May 22

Read this intro thread 🧵. CAMEO is part of SWISS-MODEL: a protein structure homology-modelling suite of software tools and databases which is one of the 17 resources in our portfolio of leading open biodata resources.

@torstenschwede.bsky.social @xavier.robin.info

CAMEO-3D @cameo3d.org · Apr 28

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

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Reposted by Janani Durairaj (Jay)

Gemma C. Atkinson @gemmaatkinson.bsky.social · May 19

Really excited to share our resource and analysis of AlphaFold-predicted monomers and homodimers across viruses and phages. Project driven by fab PhD student @rodai.bsky.social and with our great collaborators Joana Pereira @joanampereira.bsky.social and @ninjani.bsky.social

bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · May 17

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes https://www.biorxiv.org/content/10.1101/2025.05.14.653371v1

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Arne Elofsson @bioinfo.se · May 5

In this evaluation of AlphaFold3 (and other methods), we show that (i) accurate predictions are limited to RNA structures/complexes with structural similarity to PDB and (ii) that current methods are bad at estimating the accuracy of the predictions. www.biorxiv.org/content/10.1...

Limits of deep-learning-based RNA prediction methods

Motivation: In recent years, tremendous advances have been made in predicting protein structures and protein-protein interactions. However, progress in predicting the structure of RNA, either alone or...

www.biorxiv.org

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Janani Durairaj (Jay) @ninjani.bsky.social · Apr 30

Thank you for the invite, wonderful audience, and really nice event! Here are the slides for those interested: docs.google.com/presentation...

JD_AIChemist_30042025

Deep Learning for Protein and Protein-Ligand Complex Prediction Are we there yet? Jay 30.04.2025

docs.google.com

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Janani Durairaj (Jay) @ninjani.bsky.social · Apr 28

Check out CAMEOs flashy new website and features!

CAMEO-3D @cameo3d.org · Apr 28

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

2

Reposted by Janani Durairaj (Jay)

CAMEO-3D @cameo3d.org · Apr 28

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

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