Excited to report the first zero-shot designed, de novo enzyme catalyzing two of the most energetically demanding reactions in biology—phosphomonoester and phosphodiester hydrolysis—with catalytic efficiencies comparable to natural enzymes! 🚀 /🧵 @stanfordbiosci.bsky.social @simonduerr.eu

For a deeper dive, I gave a talk on AF2BIND recently at the MIA series at the Broad Institute. Check it out! Also check out Primer by talented student Ben Fry @benf549.bsky.social (not directly involved in this work). www.youtube.com/watch?v=Cjby...

I’m looking to hire a research technician for my lab at Harvard & DFCI, who would primarily work in the wet lab expressing and characterizing designed proteins, starting this summer. A great role for a recent college grad looking for an immersive research experience before grad school.

THE FIRST EPISODE OF MY SECTION 230 MINI SERIES IS HERE!!!!! Learn about what the law does, what it actually says, how it works, and who it REALLY protects

@benf549.bsky.social made a nice little google colab notebook for running LASErMPNN for protein sequence design conditioned on ligands. Check it out! Feedback welcome. colab.research.google.com/github/poliz...

The paper represents a paradigm shift by combining machine-learned interatomic potentials (MLIPs) with generative modeling to bypass traditional conformer generation, achieving both higher accuracy and greater efficiency than existing methods. Free & open source: github.com/isayevlab/LoQI

Interested in doing a postdoc at DFCI/Harvard on computationally designing and experimentally characterizing mini-protein binders for biomedical applications? Eric Fischer and I are looking for someone to work in our groups starting asap! Email me or my admin with a CV to apply!

🚨New paper 🚨 Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇 1/12

The biggest challenge for AI in biology isn't just models, it's the data used to train them. Standard biological data isn't built for AI. To unlock generative AI for drug discovery, we must rethink how we generate and capture data. 1/

📢 Congratulations 𝗗𝗿. 𝗙𝗿𝗮𝗻𝘇𝗶𝘀𝗸𝗮 𝗦𝗲𝗻𝗱𝗸𝗲𝗿 for receiving the Otto Hahn Medal and Otto Hahn Award from @maxplanck.de ! 🎉 The honors recognize her exceptional work @georghochberg.bsky.social. 🌟 Exciting times ahead! #MaxPlanck #ResearchExcellence www.mpi-marburg.mpg.de/1511259/2025...

Trying out the Boltz-2 affinity prediction on the Exatecan binders we generated with LASErMPNN and NISE. Affinity prediction still clearly has room to improve, but the model seems to be able to identify the highest affinity mutant in this small dataset. Thanks to @gcorso.bsky.social and team! 1/2

from most recent Harvard lawsuit. sums it up pretty succinctly I think

in case you missed the superb seminar that Ben Fry gave back in January, you can now check out the recording youtu.be/IgFgAYQrke4 and the preprint www.biorxiv.org/content/10.1...

We're super excited by the method. We think it can help to rapidly produce binders to small molecules for sensors, antidotes, delivery vehicles, even enzymes. Let us know what you think and please try it out! Finally, shout out to Ben and Kaia for making this all happen!!! 🤩

Lastly, Kaia checked to see if EPIC and its higher affinity mutant are able to protect exatecan from hydrolysis, which is not something serum albumin can do. For a drug that normally hydrolyzes in a few hours, EPIC was able to stabilize the lactone form for days! ✅

Since EPIC and exatecan aren't in the PDB, we wanted to see how co-structure predictors do on it. They each get the backbone right but differ at the ligand. The pose is correct but the modeling of the conformer is wonky. AF3 does the best. AF3 is also able to rank affinities via pLDDT of ligand! 😱

Kaia was able to crystalize EPIC and determine its structure to 2.0 Å resolution. It agreed pretty well with the LASEr design! RFAA had a hard time modeling the lactone ring of the drug, so there is some disagreement there. The lactone is buried as intended, and the goal was to hide it from water 👍

Ben didn't stop there. He wanted to improve affinity of EPIC for exatecan using computation alone. He used LASErMPNN to "proofread" EPIC's sequence using a predicted co-structure as input. LASEr suggested two mutations. Kaia verified that each improved binding 10x. 100x when combined (1 nM Kd)!

Kaia Slaw (no bluesky) experimentally tested 4 designs from NISE and 16 from COMBS. All 4 NISE designs bound! The highest affinity binder- which Ben and Kaia call "EPIC" - was pretty tight (0.1 uM Kd). Compared to COMBS (3 of 16 bound, tightest was 10 uM), NISE and LASErMPNN did a much better job!

Ben used NISE and LASErMPNN to design binders to exatecan, an anticancer drug prone to inactivation by hydrolysis. We also used a more "traditional" approach using COMBS and Rosetta to design binders. We could compare the methods head to head.

With the new co-structure predictors like RFAA, Boltz-1, and AF3, we can now extend self-consistency into the ligand dimension. And Ben's NISE algorithm maximizes this. Code repo here: github.com/polizzilab/N...

We all know in protein design about the goal of self consistency. That is, we want the predicted structure to look like the structure for which we designed the sequence.

Ben used LASErMPNN in combination with a protein-ligand co-structure predictor, RFAA, in an iterative algorithm called NISE that refines designs. NISE optimizes the sequence, structure, and ligand conformer together to improve the confidence of both models. It's a neural-network-only algorithm

Ben Fry (@benf549.bsky.social) was excited when proteinMPNN came out, which motivated him to train a new gNN called LASErMPNN to design sequences given protein-ligand co-structure. LASErMPNN does pretty well at this! The repo is available and even has the training code! github.com/polizzilab/L...

Super excited to share a new preprint from our lab on design of small-molecule binding proteins using neural networks! The paper has a bit of everything. A new graph neural network, new design algorithms, and experimental validation. www.biorxiv.org/content/10.1... 🧵🧪