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Timothy P. Jenkins @tpjenkins.bsky.social · Jul 31

🧪🐍 AI vs venom!
Our Nature paper with David Baker shows AI-designed proteins can block deadly snake toxins. Now featured by Reuters! 🎥
✅ 80–100% survival in mice
💸 Cheap, fast, scalable
🌍 A step toward better antivenoms

📄 www.nature.com/articles/s41...
🎬 youtu.be/gnvEDMEr2mc

AI-designed antivenom could offer new hope for snakebite victims | REUTERS

YouTube video by Reuters

youtu.be

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Timothy P. Jenkins @tpjenkins.bsky.social · Jul 24

We believe this approach can accelerate the development of safer, more effective immunotherapies for patients.
And a special thank you to the talented @mfernandezquintero.bsky.social & Johannes Loeffler for the stunning graphic! 🎨
#CancerResearch #Immunotherapy #AI

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Timothy P. Jenkins @tpjenkins.bsky.social · Jul 24

This was a monumental team effort bringing together immunology, computational biology, and structural biology.

A huge congratulations to the incredible teams at DTU HealthTech, DTU Bioengineering, & @scripps.edu and to all my brilliant co-authors, especially @Kristoffer Haurum Johansen.

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Timothy P. Jenkins @tpjenkins.bsky.social · Jul 24

Our platform's key achievements include:
⚡️ Speed: A rapid 4-6 week pipeline from computer design to validated lab result. 
🎯 Precision: An AI-driven process to screen for specificity & reduce off-target risks. 
🤝 Personalization: It works even for a patient's unique tumor mutation.

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Timothy P. Jenkins @tpjenkins.bsky.social · Jul 24

In this work, we designed completely novel proteins, or ‘minibinders,’ from scratch. 🤖

These act as a high-precision guidance system, leading a patient's own T-cells (black) to recognize and destroy cancer cells (red) with remarkable accuracy.

#ProteinDesign #GenerativeAI

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Timothy P. Jenkins @tpjenkins.bsky.social · Jul 24

Thrilled to announce our paper, "De novo-designed pMHC binders facilitate T cell-mediated cytotoxicity toward cancer cells," is officially out in @science.org!

We used generative AI to build a 'GPS' for immune cells to hunt cancer.

Read it here: doi.org/10.1126/scie...

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Timothy P. Jenkins @tpjenkins.bsky.social · Jul 16

While I’m bouncing between emails and desperately waiting for my holiday, it’s good to know at least something in the lab is holding it together.

Thermal stability might not be glamorous, but it’s underrated.

Designerbodies: even when things get heated, still doing their job ;)

AffinityAI @affinityaibio.bsky.social · Jul 16

Whether you're on holiday 🏖️ or still in the lab 🧪 trying to keep cool, at least one thing isn't melting: our DesignerBodies.

Generatively designed. Thermally stable ❄️ Reliable reagents that don’t need a break 💪

#ProteinDesign #AI #Biotech

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Timothy P. Jenkins @tpjenkins.bsky.social · Jul 16

Built for heat. Unlike me;)

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Timothy P. Jenkins @tpjenkins.bsky.social · Jun 11

Designing binders instead of screening for months? Can’t wait to disappoint reviewers in new and innovative ways.

Timothy P. Jenkins @tpjenkins.bsky.social · Jun 11

At AffinityAI we’re moving from “finders keepers” to “designers binders”, one generative model at a time.

If you could have a binder to anything, what would it be?

(Proteins, obscure signalling pathways, that one reviewer who never gets back to you…;)

AffinityAI @affinityaibio.bsky.social · Jun 11

We’re rethinking what a binding reagent can be.

Most antibodies weren’t designed, they were discovered. At AffinityAI, we’re flipping that logic: we build binders from first principles, guided by generative AI.

What targets would you be interested in having a binder to?

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Reposted by Timothy P. Jenkins

AffinityAI @affinityaibio.bsky.social · Jun 2

Ægget redefined the lounge.
We're redefining what it means to design a protein.

At AffinityAI, we combine Danish design sensibilities with precision molecular engineering. Elegant. Efficient. Engineered to bind.

🧬 Discover how we’re reshaping molecular function:

www.affinityai.bio

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Timothy P. Jenkins @tpjenkins.bsky.social · May 30

💡 Curious about:
– How generative AI is transforming protein research?
– Why mass spec is such a rich (but messy) playground for AI?
– What it takes to go from spectrum to sequence to structure?

Give it a listen 🎧

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Timothy P. Jenkins @tpjenkins.bsky.social · May 30

We focus on our new Nature Machine Intelligence paper introducing InstaNovo — a transformer model for de novo peptide sequencing from mass spectrometry. No reference database needed.
📄 www.nature.com/articles/s42...

InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments - Nature Machine Intelligence

InstaNovo, a transformer-based model, and InstaNovo+, a multinomial diffusion model, enhance de novo peptide sequencing, enabling discovery of novel peptides, improved therapeutics sequencing coverage...

www.nature.com

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Timothy P. Jenkins @tpjenkins.bsky.social · May 30

🎧 Had the pleasure of joining Anders Høeg Nissen on the AI Denmark Podcast to talk about how we’re using AI to crack the protein code 🧬

Catch my segment from 9:30 (and yes — it’s in English 😉)
🎙️ open.spotify.com/episode/4g3R...

AI giver proteinforskningen turboboost

AI Denmark · Episode

open.spotify.com

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Timothy P. Jenkins @tpjenkins.bsky.social · May 16

Great to see #AffinityAI represented by Esperanza and Oliver at the DTU Startup Day 💪

Lots of interest in what we’re building, especially the fact that we deliver #real #reagents rather than just #AI predictions.

Excited for what's to come!

AffinityAI @affinityaibio.bsky.social · May 16

Great energy at DTU Startup Day 🎉
Big thanks to @DTUSkylab for bringing together researchers, investors, and innovators.
We had a blast sharing what we're building at AffinityAI.

#AffinityAI #DTUSkylab #StartupLife

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Timothy P. Jenkins @tpjenkins.bsky.social · May 14

🚨 We’re hiring a PhD student! 🚨

Join us at DTU Bioengineering + collaborators Messoud & Håkan Ashina + Esperanza Rivera de Torre to bring preventative migraine therapeutics from 💻 to 🧠

🔗 Apply: lnkd.in/dCRU_EN3

🔍 Project: lnkd.in/dbpi8MwX

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Timothy P. Jenkins @tpjenkins.bsky.social · May 12

🚨 Big news! We’ve received a NovoNordisk Foundation Tandem Grant for #MIGRAINE — designing #AI-powered #GPCR-targeting biologics for chronic migraine. From computer to human in 4 years. Proud to team up with Messoud and Hakan Ashina, as well as Esperanza Rivera de Torre!
🧠 + 💊 + 🧬 = new hope.

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Timothy P. Jenkins @tpjenkins.bsky.social · May 8

We’re already supporting:
– Proteins that are hard to purify
– Assays that demand specificity
– Targets that need quantitative detection

Please reach out if you want to hear more.
#StartupLaunch #Founder #AffinityAI

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Timothy P. Jenkins @tpjenkins.bsky.social · May 8

What we offer:
– Designerbodies™ with pM–nM affinity
– ARCANE™ designs for affinity, stability, and expression
– RAVEN™ screens candidates at scale
Built for diagnostics, therapeutics, and biotech pipelines.
#AIinBiotech #SyntheticBiology

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Timothy P. Jenkins @tpjenkins.bsky.social · May 8

🚀 Big news: AffinityAI is live
We’ve built a platform for custom protein binders, AI-designed, in vitro validated, and entirely animal-free.
I'm proud to lead this as CEO.
🔗 affinityai.org

#AffinityAI #Biotech #ProteinEngineering

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Timothy P. Jenkins @tpjenkins.bsky.social · Apr 9

3/
v1.1 generalises well:
In a GluC-treated HeLa dataset, we reached 81.3% peptide recall—higher depth, same model.

Improved confidence metrics = better precision, fewer false positives, more IDs.
Code: bit.ly/43ExRGI

bit.ly

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Timothy P. Jenkins @tpjenkins.bsky.social · Apr 9

2/
What’s new in InstaNovo v1.1?

🧬 +13.5% recall
🎯 +42.6% more exact PSMs
🔍 145% more peptides & 35% more proteins @ 5% FDR
🧪 Support for 7 PTMs: phosphorylation, deamidation, carbamylation, ammonia loss, oxidation, acetylation, carbamidomethylation

Paper: bit.ly/3XBeJFh

InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments - Nature Machine Intelligence

InstaNovo, a transformer-based model, and InstaNovo+, a multinomial diffusion model, enhance de novo peptide sequencing, enabling discovery of novel peptides, improved therapeutics sequencing coverage...

bit.ly

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Timothy P. Jenkins @tpjenkins.bsky.social · Apr 9

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🚀 InstaNovo just got a major upgrade.

Our Nature Machine Intelligence paper with @instadeepai presents v0.1—but while the paper was under review, we kept building.

Now releasing InstaNovo v1.1, with major gains.
Blog: bit.ly/4lircYB

🧵

Introducing the next generation of InstaNovo models

Since our InstaNovo paper is now published, we’d like to share an update on what we’ve been working on while our manuscript was under review. With the release of our preprint over a year ago, we were ...

bit.ly

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Reposted by Timothy P. Jenkins

Andreas H. Laustsen-Kiel @andreaslaustsen.bsky.social · Mar 20

I am very excited to announce the publication of this new research article on "Orally delivered toxin–binding protein protects against diarrhoea in a murine cholera model", which is a topic I sincerely care about: nature.com/articles/s41...
Thanks to all co-authors and funders!

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Reposted by Timothy P. Jenkins

Andreas H. Laustsen-Kiel @andreaslaustsen.bsky.social · Mar 31

Excited to share a new paper in Nature Machine Intelligence that I had the pleasure of contributing to, alongside great collaborators from Europe!

InstaNovo is a deep learning model for de novo peptide sequencing — pushing proteomics beyond databases.

📄 www.nature.com/articles/s42...

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