@IanRHum

Computational structural biology. PhD from Baker lab @UWproteindesign

 Seattle, WA
Joined May 2018
  • Tweets103
  • Following187
  • Followers539
5Media
Ian Humphreys retweeted
Yo Akiyama@yoakiyamaJul 21
Excited to share our now published manuscript @CellCellPress highlighting advances in modeling the evolution of protein-protein interactions with MSA Pairformer. Big thanks to @ZhidianZ, @oliviatang116, @eunbelivable, Milot Mirdita, Martin Steinegger, and @sokrypton !🧵 (1/10) cell.com/cell/fulltext/S0092…

Expanding the scope of protein language modeling to protein-protein interactions with MSA Pairformer

Protein language models have excelled at modeling individual proteins, but extending these capabilities to protein complexes remains a major challenge. MSA Pairformer, a parameter-efficient protein...

cell.com
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Ian Humphreys retweeted
Jing Zhang@jzhang_genome27 Sep 2025
Predicting protein-protein interactions in the human proteome | Science science.org/doi/10.1126/scie…

Predicting protein-protein interactions in the human proteome

Protein-protein interactions (PPIs) are essential for biological function. Coevolutionary analysis and deep-learning (DL)–based protein structure prediction have enabled comprehensive PPI identific...

science.org
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Ian Humphreys retweeted
Andrew Favor@andrew_favor3 Oct 2025
We are pleased to share our new preprint: “De novo design of RNA and nucleoprotein complexes”. This work extends the principles of de novo protein design to RNA and DNA, enabling the generative design of complex multi-polymer structures! (1/6) doi.org/10.1101/2025.10.01.6…
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Ian Humphreys retweeted
Green Ahn@Green_Ahn1 Oct 2025
pH gradients are central to physiology, from vesicle acidification to the acidic tumor microenvironment. But how do we program proteins to respond to pH? In our new preprint biorxiv.org/content/10.1101/…, we developed computational methods to rationally design pH-sensitive binders. 🧵

Computational design of pH-sensitive binders

pH gradients are central to physiology, from vesicle acidification to the acidic tumor microenvironment. While therapeutics have been developed to exploit these pH changes to modulate activity across...

biorxiv.org
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Ian Humphreys retweeted
Magnus Bauer@kinasekid30 Sep 2025
Phosphorylation on tyrosines control key pathways in immunity, cancer, and metabolism. For the first time, we can now design proteins that specifically recognize individual phosphotyrosines, even in disordered regions. (1/8) Preprint: biorxiv.org/content/10.1101/…
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We sought to make proteins both potent and FAST. We used #proteindesign to design precise control over protein interaction lifetimes, enabling us to construct rapid-response circuits, biosensors, and switchable cytokines. Now published @Nature! Links to paper and tutorial below.
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Ian Humphreys retweeted
Rohith Krishna@r_krishna319 Sep 2025
We asked ourselves what could we do if we worked cooperatively as a team to create a single model that could design any biomolecular interactions. Yesterday, we reported details of RFdiffusion3, the next step towards building functional proteins straight from the computer.
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Very excited to share our paper "De novo Design of All-atom Biomolecular Interactions with RFdiffusion3", now on BioRXiv. biorxiv.org/content/10.1101/… 1/n
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Ian Humphreys retweeted
Rohith Krishna@r_krishna310 Sep 2025
We built RF3 with @nvidia’s latest cuEquivariance accelerations, letting us iterate fast. Now we’re sharing the full stack: ModelForge — open-source infra for training biomolecular AI. Start your project here 👉 github.com/RosettaCommons/mo…

GitHub - RosettaCommons/foundry: Central repository for biomolecular foundation models with shared...

Central repository for biomolecular foundation models with shared trainers and pipeline components - RosettaCommons/foundry

github.com
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Ian Humphreys retweeted
Yo Akiyama@yoakiyama5 Aug 2025
Excited to share work with @ZhidianZ, Milot Mirdita, Martin Steinegger, and @sokrypton biorxiv.org/content/10.1101/… 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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Ian Humphreys retweeted
Pushmeet Kohli
@pushmeet11 Nov 2024
The #AlphaFold 3 model code and weights are now available for academic use. We @GoogleDeepMind are excited to see how the research community continues to use AlphaFold to address open questions in biology and new lines of research. github.com/google-deepmind/a…

GitHub - google-deepmind/alphafold3: AlphaFold 3 inference pipeline.

AlphaFold 3 inference pipeline. Contribute to google-deepmind/alphafold3 development by creating an account on GitHub.

github.com
Pushmeet Kohli
@pushmeet13 May 2024
We love the excitement & results from the community on AlphaFold 3 and are doubling the AF Server daily job limit to 20. Happy to also share that we're working on releasing the AF3 model (incl weights) for academic use, which doesn’t depend on our research infra, within 6 months.
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Ian Humphreys retweeted
The Nobel Prize
@NobelPrize9 Oct 2024
BREAKING NEWS The Royal Swedish Academy of Sciences has decided to award the 2024 #NobelPrize in Chemistry with one half to David Baker “for computational protein design” and the other half jointly to Demis Hassabis and John M. Jumper “for protein structure prediction.”
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Ian Humphreys retweeted
Yang Hsia@yhsia_ipd9 Oct 2024
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Exciting new work from Qian Cong's group on predicting human protein interactome. Leveraging new eukaryotic genomes, new RoseTTAFold2 trained on +/- pairs of PPI and large distilled dataset of domain-domain interactions! 🤩 biorxiv.org/content/10.1101/…
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Ian Humphreys retweeted
Linna An@alchemist_an2 Oct 2024
Computing the Human Interactome biorxiv.org/content/10.1101/… Jing, @IanRHum, Qian, amazing work!

Computing the Human Interactome

Protein-protein interactions (PPI) are essential for biological function. Recent advances in coevolutionary analysis and Deep Learning (DL) based protein structure prediction have enabled comprehen...

biorxiv.org
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Ian Humphreys retweeted
Minkyung Baek
@minkbaek2 Oct 2024
Happy to share our preprint on predicting human protein interactome! We've trained RoseTTAFold2-PPI on both positive/negative PPI pairs. We also extended the training set by utilizing domain-domain interactions from predicted structures. biorxiv.org/content/10.1101/…

Computing the Human Interactome

Protein-protein interactions (PPI) are essential for biological function. Recent advances in coevolutionary analysis and Deep Learning (DL) based protein structure prediction have enabled comprehen...

biorxiv.org
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Ian Humphreys retweeted
Jing Zhang@jzhang_genome2 Oct 2024
Excited to share our latest research on human PPI now available on bioRxiv! Check it out: biorxiv.org/content/10.1101/… #Bioinformatics #Research #ScientificPaper"

Computing the Human Interactome

Protein-protein interactions (PPI) are essential for biological function. Recent advances in coevolutionary analysis and Deep Learning (DL) based protein structure prediction have enabled comprehen...

biorxiv.org
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Ian Humphreys retweeted
Jing Zhang@jzhang_genome20 Sep 2024
Our "Protein interactions in human pathogens revealed through deep learning" in Nature Micriobiology finally got online. 🎉🎉🎉Read here: nature.com/articles/s41564-0…

Protein interactions in human pathogens revealed through deep learning

Nature Microbiology - RoseTTAFold2-Lite uses residue–residue coevolution and protein structure prediction to identify and structurally characterize protein–protein interactions in...

nature.com
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Ian Humphreys retweeted
King Lab
@KingLabIPD5 Sep 2024
#MERS vaccines built on our two-component protein nanoparticle platform induce robust neutralizing antibody responses and protect mice against vaccine-matched challenge. This collaborative project was led by @chao_cara and is out now on @biorxivpreprint: biorxiv.org/content/10.1101/…

Protein nanoparticle vaccines induce potent neutralizing antibody responses against MERS-CoV

Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic betacoronavirus that causes severe and often lethal respiratory illness in humans. The MERS-CoV spike (S) protein is the viral...

biorxiv.org
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Excited to announce our new paper on designing allosterically regulated protein assemblies from scratch, now published in @Nature! This collaborative effort included key contributions from @FloPraetorius, Abbas Idris, @AnnikaPhilomin, @cweidle1 and others! nature.com/articles/s41586-0…

De novo design of allosterically switchable protein assemblies

Nature - We investigate the de novo design of allostery and suggest that it can arise from global coupling of the energetics of protein substructures without optimized allosteric communication...

nature.com
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