Could we accelerate the discovery of the next GLP-1R agonist? 🚀 Here, we introduce PepTune, a multi-objective guided discrete diffusion model that generates target-specific peptides, while optimizing their therapeutic properties! 🪐

📜: arxiv.org/abs/2412.17780
💻: huggingface.co/ChatterjeeLa...

So excited to host the 2nd GEM Workshop at ICLR 2025! 🎉 We have amazing speakers/panelists 🧑‍🔬, money for new AI+Experiment collabs 🤑, and we're partnering with @naturebiotech.bsky.social to get the best papers into review! 📜 Definitely submit your new work and see you in Singapore!! 🇸🇬

So excited to have Christian (@machine.learning.bio) join us at Duke!! 💙 We're building such an amazing AIxBio community with @rohitsingh8080.bsky.social, @alextong.bsky.social, Phil Romero, and others. ESPECIALLY in all things bio-based language models! 💻 🧬 Come join us in Durham! 😈

🚨 Current graduate students! If you're interested in developing and leveraging generative language models for therapeutics design, please apply to the
FutureHouse's postdoctoral fellowship and indicate my lab as an option! 😃 $125k salary and access to all of their amazing resources! 🌟

Surreal! 🤩 With co-founders Martin and Dina, we started Gameto in 2020 with just a silly graph theory algorithm I developed to predict TFs that could differentiate ovarian cells. 💻➡️🧫 Now, little Mia is here with the tech that has grown out of that work. 🐣 So proud!! 🥰
www.forbes.com/sites/alexyo...

Any AIxBio folks at NeurIPS and want to meet up with me and the lab? So many of our best collaborations have come from meetings at NeurIPS, ICML, and ICLR!! 🌟

We are so grateful to #EndAxD for funding our research leveraging generative language models to design peptide-guided degraders of dysregulated GFAP! 🙏 Please share and consider giving to this wonderful, grassroots organization. 💫 endaxd.org

#EndAxD Instagram Post: www.instagram.com/p/DC7sV2GPst...

Try out Fred's (my PhD student) reimplementation ESM2 with FlashAttention, achieving up to 60% memory savings and 70% faster inference! 🚀 No need to change your ESM code — it’s API-compatible! github.com/pengzhangzhi...

Alright new BlueSky friends, need some advice! 💡 I’m teaching my Generative Models (pLMs, graph models, diffusion, etc.) class at Duke next semester, and want to mix it up! Question: should I do theory on the board ✏️+ live coding 🧑🏾‍💻, or pre-prepared slides 🖥️ with annotated code snippets?

New RFDiffusion-for-peptide (RFpeptide) paper from @gauravbhardwaj.bsky.social and team at @uwproteindesign.bsky.social! 🌟 Beautiful binding data on 4 highly-structured targets (pLDDT > 90)! 🙌🏾 Not too confident this would work on highly disordered targets, though. 🤔

www.biorxiv.org/content/10.1...

I’m curious to see how all of the new AF3 mimics perform. 🧐 My lab’s been installing them on our servers, and faster inference and ease-of-use are key for us. Boltz-1 has an early lead, but nothing beats a good frozen pLM with a structure trunk! 😅 Bc accuracy to the PDB isn’t the best metric. 🤷🏾‍♂️

Hi new followers! 🥰You may know me from Twitter as the sequence-first, pLM guy — hope you will continue to follow my lab’s work! 🥹 While you’re here, check out my lab’s new preprint on delivering pLM-generated degraders via LNPs to degrade cytosolic β-catenin in vivo! www.biorxiv.org/content/10.1...

SaLT&PepPr is published in
Communications Biology! Here, we fine-tune the ESM-2 pLM to identify peptidic binding sites on target-interacting partner sequences. We fuse these "guide" peptides to E3 ubiquitin ligases to degrade disease-causing proteins! Take a read! :) www.nature.com/articles/s42...

Happy to share our early work on generating binding peptides conditioned ONLY on the target sequence! 🌟 PepMLM masks cognate peptides at the end of target protein sequences, and tasks ESM-2 to fully reconstruct the binder region. 😷 arxiv.org/abs/2310.03842

“PepMLM: Target Sequence-Conditioned Generation of Peptide Binders via Masked Language Modeling” 🧶🧬

Fine-tunes ESM-2 network to achieve “target-conditioned de novo binder design from sequence alone”

arxiv.org/abs/2310.03842
huggingface.co/TianlaiChen/...