Really cool approach to find an update to the Rosetta energy function ("-beta_jan25"):

Results are in, and it looks like the only category with a spearman correlation > 0.4 is hydrophobicity 😅
huggingface.co/spaces/ginkg...

Pretty cool use case for de novo binders:

Guiding Generative Models for Protein Design: Prompting, Steering and Aligning

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Guiding Generative Models for Protein Design: Prompting, Steering and Aligning [new]
Reviews methods to guide generative models to design proteins with specific properties, even if rare in training data. Focuses on parameter and fixed-model methods.

Today is the last day of the Ginkgo antibody developability challenge, curious to see whether someone came up with a deep learning approach that actually out competes the biophysical baselines
github.com/ginkgobiowor...

De novo design of phospho-tyrosine peptide binders

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De novo design of phospho-tyrosine peptide binders [new]
Designs binders for phosphorylated tyrosine sites on clinically relevant targets using a deep generative framework, enabling modulation of signaling pathways.

Super excited for the full data, especially to see which of the over 400 screened binders actually got us the third place 🥳
Shout-out to the organizers for this very cool competition!

NaturalAntibody+BI benchmarking IF models on internal antibody data:

"... IF models are moderately useful in an industrial setting for filtering NGS datasets."

Also from their data antibody-specific models seem to be better than their base models and antigens don't substantially alter predictions

Also shout-out to @gbouras13.bsky.social for having the code available on GitHub even long before the preprint

Really cool to see this out!
As someone with a more structural background looking for a phage genome annotation tool this was more than I'd ever hoped for 😄

In 1965, Margaret Dayhoff published the Atlas of Protein Sequence and Structure, which collated the 65 proteins whose amino acid sequences were then known.

Inspired by that Atlas, today we are releasing the Dayhoff Atlas of protein sequence data and protein language models.

The open-source Masala software suite: Facilitating rapid methods development for synthetic heteropolymer design Although canonical protein design has benefited from machine learning methods trained on databases of protein sequences and structures, synthetic heteropolymer design still relies heavily on physics-b...

We have a new preprint out on the Masala software suite, a free and open-source platform for easy biomolecular modelling methods development. www.biorxiv.org/content/10.1...

We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!

github.com/martinpacesa...

How to train your model Event dates Sunday 8/3 1pm - 10pm Monday 8/4 7am - 2pm Friday 8/8 9am-10pm Saturday 8/9 Travel Application Link This immersive, hands-on event is designed for researchers who are ready to move beyo...

Register for SRC25 Workshop (tinyurl.com/SRC25-worksh...) : How to train your model - This immersive, hands-on advanced-level event is designed for researchers who are ready to move beyond “out-of-the-box” machine learning models for protein design.

1-day Protein Design Workshop @ SRC 2025 AI-Driven Design of Biologics: Hands-on Guide to Using State-of-the-Art ML Protein Models brought to you by the Rosetta Commons Event dates Sunday 8/3 1pm - 6 pm Monday 8/4 8am - 2 pm Event Locati...

One-day novice-level course surveying popular tools and workflow for modern protein design with brief exploration of common applications including antibody design and binder design: 1-day Protein Design Workshop. Register here: tinyurl.com/SRC25-worksh...

Thrilled to announce that this year’s European RosettaCon protein design conference will take place in Ljubljana, Oct 20–22, 2025!

Open to all, with a remote keynote by Nobel laureate David Baker.

More info coming soon — it’s going to be amazing! Hope to see you there!

The Praetorius lab for Biomolecular Design at the Institute of Science and Technology Austria (ISTA) is looking for grad students in 2024. If you are interested in protein design at a great institute near Vienna reach out to me!
www.dropbox.com/scl/fi/6iny2...