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Alexander Ille @alexander-ille.bsky.social · Aug 27

State of the art!

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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Alexander Ille @alexander-ille.bsky.social · Aug 21

Excited to share an update of our work on modeling the human protein interactome in 3D using Boltz-2. Large-scale protein complex prediction allows for exploring structurally-informed biological networks.

Preprint on bioRxiv: doi.org/10.1101/2025...

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Reposted by Alexander Ille

RCSB Protein Data Bank @rcsbpdb.bsky.social · Aug 20

Eat your carrots or you'll go blind! The biochemical reason for this warning is that we need retinal, vitamin A, to form the pigment that absorbs light in our eyes.
More at Molecule of the Month: pdb101.rcsb.org/motm/66
#PeakPerformance

Vitamin A plays a crucial role in vision by converting light into electrical signals. At the heart of this process are rhodopsin proteins (purple) found in the retina, a light-sensing tissue at the back of the eye. Vitamin A is the precursor to retinal (yellow), which is nestled within the active site of rhodopsin. When light strikes retinal, it transforms from its cis form to its trans form (see inset), allowing rhodopsin to bind and activate its associated G-protein complex (green). This process sets off a cascade of events that ultimately leads to the perception of light.
Visit the 2025 Calendar: The Structural Biology of Nutrition to learn more.
Illustration by RCSB PDB intern Xinyi Christine Zhang.

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Alexander Ille @alexander-ille.bsky.social · Jul 4

Excited to share our work on modeling the human protein interactome in 3D. This currently includes 1,394 interaction structures predicted with Boltz-2. Grateful for the open-access resources making this possible!

Preprint: doi.org/10.1101/2025...

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Alexander Ille @alexander-ille.bsky.social · Jun 24

The prediction of protein conformational dynamics from sequence is expected to have broad utility across biological and medical research. Huge thank you to my co-authors for contributing to this piece!

Alexander Ille @alexander-ille.bsky.social · Jun 24

Importantly, there is an abundance of sequence data and increasing availability of conformationally-sensitive structure data which may be leveraged for AI/ML model training.

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Alexander Ille @alexander-ille.bsky.social · Jun 24

Based on the above conjecture, AI/ML models may be developed to predict a protein’s conformational dynamics from its sequence. We provide a conceptual architecture for such a model, drawing from previous work which provides encouraging precedent.

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Alexander Ille @alexander-ille.bsky.social · Jun 24

In the current piece, we consider that biological sequence encodes not only static 3D structure, but also conformational dynamics. This is important because inside of a cell, things aren’t static and motionless, they are constantly moving around.

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Alexander Ille @alexander-ille.bsky.social · Jun 24

Later on, Christian Anfinsen proposed that “the native conformation is determined by the totality of interatomic interactions and hence by the amino acid sequence” (Anfinsen, 1973).

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Alexander Ille @alexander-ille.bsky.social · Jun 24

On the relationship between sequence and structure, Francis Crick speculated that “folding is simply a function of the order of the amino acids” (Crick, 1958).

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Alexander Ille @alexander-ille.bsky.social · Jun 24

Excited to share a new article I co-authored on the relationship between biological sequence and structure! We look back to historic hypotheses, and look forward to how AI/ML models may be developed to predict protein conformational dynamics. Paper: doi.org/10.1063/4.00...

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Alexander Ille @alexander-ille.bsky.social · Jun 18

Hemoglobin, the biomolecule that breathes, modeled with Boltz-2.

With the recent release of #Boltz2, I gave it a try for modeling hemoglobin. Hemoglobin structures were likely included for training, and this was just a fun test, but it’s awesome to see this modeling in action!

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Alexander Ille @alexander-ille.bsky.social · Jun 8

Truly remarkable work. Looking forward to using it!

Gabriele Corso @gcorso.bsky.social · Jun 6

Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A thread… 🤗🚀

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Alexander Ille @alexander-ille.bsky.social · May 16

Dynamic insight into DNA → RNA → protein. Great work!

Olivier Duss @olivierduss.bsky.social · Dec 4

First paper of our lab today @natureportfolio.bsky.social by Nussi!

We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!

@embl.org #RNAbiology #RNASky

t.co/a24Xxcxdo0