Next week, Jeffrey Chang from @nickpolizzi.bsky.social's lab will present cutting-edge work from a pre-print that just came out today! Wednesday, August 12th 2026, 7pm EDT in Room 6055, Longwood Center, @danafarber.bsky.social "De novo design of small-molecule-induced conformational change"

De novo design of small-molecule-induced conformational change

Many biological proteins function by changing shape upon small-molecule binding. Here, we present a general strategy for designing de novo proteins that undergo small-molecule-induced conformational c...

biorxiv.org

We can design "static" binders routinely now, but design of "dynamic" shape-changing proteins has remained quite hard. Jeffrey Chang and I asked: why can't we couple small-molecule binding to shape change? After all, natural proteins do it every day. In a new preprint, we show how it can be done. 🧵

Can protein dynamics help guide protein engineering? Our latest paper shows that a simple NMR peak intensity analysis can reveal functional dynamics hotspots, helping to uncover promising engineering targets. With @thompson-lab.bsky.social and Natalie Goto. doi.org/10.1093/prot...

Mapping functional dynamics hotspots for protein engineering with NMR peak intensity analysis

Abstract. Structural dynamics play a crucial role in protein function, and tuning these dynamics through mutagenesis has emerged as a promising strategy fo

academic.oup.com

I hope everyone had a great 4th of July, and we've got a great seminar for you this week by James Roney from @sokrypton.org's lab! Join us this Wednesday, July 8th 2026 at 7pm EDT in Room 181, Building 68, @mit.edu "Energy-Based Models of Protein Structure, Dynamics, and Folding" bpdmc.org

schedule

introduction and membership Boston Protein Design and Modeling Club (BPDMC) is a community of computational protein engineers and modelers from both academia and industry. While we are based in Boston...

bpdmc.org

De novo designed oligomers that respond to copper, small molecules, and phosphorylation... Using a single design strategy? 🧬⚙️ 🎉 Excited to share our new bioRxiv preprint—a collaboration between the Khmelinskaia, Correia, Schoeder and a Tinnefeld labs! www.biorxiv.org/content/10.6...

A generalizable interface-seeded framework for de novo design of functional oligomers

Protein oligomers are ubiquitous in biological systems and essential for function. However, the de novo design of oligomers that controllably assemble in response to exogenous stimuli remains challeng...

biorxiv.org

If you weren't able to make it out to MIT last month for Foster Birnbaum's outstanding seminar, you can now check out the recording 👇 youtu.be/w-NddBw2FJk

Beyond sequence recovery: Improved modeling of the sequence-energy landscape of protein structures

YouTube video by Boston Protein Design and Modeling Club

youtu.be

Check out the nice commentary on our paper from @dereklowe.bsky.social Thanks for the spotlight, Derek! www.science.org/content/blog...

Here's a Ligand, Go Design a Protein

science.org

Out now as a preprint, “Molecular basis of mitochondrial leucine transport by human Sideroflexin 1”. #CryoEM #Mitochondria #StructuralBiology www.biorxiv.org/content/10.6...

Our lab's paper on the de novo design of small-molecule binding proteins is out! In it, we show how neural nets can be trained and used to design binders to drugs with very high success rates. www.nature.com/articles/s41...

Zero-shot design of drug-binding proteins via neural iterative selection−expansion - Nature

 By pairing two neural networks in an iterative optimization algorithm, small-molecule binding proteins can be designed from scratch with high accuracy, affinity and success rates, showing p...

nature.com

New research published in @nature.com by @danafarber.bsky.social’s @nickpolizzi.bsky.social describes a deep-learning-based algorithm that accurately designs drug-binding proteins from scratch, which could make cancer therapy safer. Read more: bit.ly/4wbEURV

Come join the new Novo Nordisk Foundation Center for Protein Design as a group leader Cool science in a great scientific environment in wonderful and very family friendly Copenhagen There are two positions that can either be at TT assistant or associate prof level employment.ku.dk/tenure-track...

Tenure-track Assistant Professor or Associate Professor of De novo Protein Design

The Novo Nordisk Foundation Center for Protein Design at the University of Copenhagen seeks to appoint two new group leaders in de novo protein design from 1 February 2027 or as soon as possible thereafter. These positions will be at the Assistant or Associate Professor level and associated with the Department of Biology (Faculty of Science) or the Department of Drug Design and Pharmacology (Faculty of Health and Medical Sciences).

employment.ku.dk

We've got an outstanding seminar for you this Wednesday, June 10th 2026 at 7pm EDT in Room 181, Building 68, @mit.edu Foster Birnbaum from @keatinglab.bsky.social "Beyond native sequence recovery: Improved modeling of the sequence-energy landscape of protein structures" bpdmc.org

schedule

introduction and membership Boston Protein Design and Modeling Club (BPDMC) is a community of computational protein engineers and modelers from both academia and industry. While we are based in Boston...

bpdmc.org

Spin-Dependent Extracellular Respiration https://www.biorxiv.org/content/10.64898/2026.05.29.728850v1

In the W-S lab's first preprint, we describe how genomic language models know something about RNA thermodynamics. Though we think this is cool, things get tricky! A growing practice for interpreting LMs is to perturb input tokens, often called "Categorical Jacobian": 👇

Are you interested in understanding protein dynamics and allostery in biomedically relevant "loopy" enzymes? We are looking for postdocs to join our group at GT for both applied and method development work. If you are interested, please email me your CV, cover letter, and details of 2-3 referees.

Researchers pioneer method to rapidly design proteins Their strategy revealed new details that open the door to designing proteins with powerful abilities that could ultimately benefit medicine and manufacturing.

Researchers pioneer method to rapidly design proteins

Their strategy revealed new details that open the door to designing proteins with powerful abilities that could ultimately benefit medicine and manufacturing.

www6.slac.stanford.edu

One, perhaps two, of our postdocs are moving on to faculty positions this year (more news soon!). While they're truly irreplaceable, it does mean that we have openings for new members to join our team studying #cilia. If interested, please apply: academicpositions.harvard.edu/postings/15526

Happy to share this in its published form! More than any project I've worked on, this was a huge team effort, so thank you so much to that team! Especially @ajrferrari.bsky.social www.nature.com/articles/s41...

Large-scale discovery, analysis and design of protein energy landscapes - Nature

An analysis of 5,778 domains 28–64 amino acids in length reveals hidden variation in conformational fluctuations, even between sequences sharing the same fold and global folding stability.

nature.com

Gabriel Rocklin@grocklin.bsky.social · last yr.

Small proteins can be more complex than they look! We know proteins fluctuate between different conformations- but by how much? How does it vary from protein to protein? Can highly stable domains have low stability segments? @ajrferrari.bsky.social experimentally tested >5,000 domains to find out!

De novo design of transmembrane accessory subunits for fold stabilization and expansion https://www.biorxiv.org/content/10.64898/2026.05.14.725059v1

Ariel Tennenhouse gave a stellar talk this week! Don't fret if you weren't in the room last Wednesday night because you can check out the recording 👇 youtu.be/cQu6yUZINgo

How can AI help accelerate cancer research? Our researchers have developed an AI tool that could help speed up the search for drug targets, potentially overcoming a major bottleneck in cancer drug discovery.

AI Tool Could Speed Discovery of New Cancer Drug Targets 

Al tools could speed discovery of new cancer drug targets by analyzing complex data, helping researchers identify treatments faster and more precisely

bit.ly

We managed to line up another fantastic speaker from out of town this month thanks to #PEGSBoston! Come see Ariel Tennenhouse present on Wednesday, May 13th 2026 at 7pm EDT in Room 181, Building 68, @mit.edu "Computational design of antibody repertoires" bpdmc.org

schedule

introduction and membership Boston Protein Design and Modeling Club (BPDMC) is a community of computational protein engineers and modelers from both academia and industry. While we are based in Boston...

bpdmc.org

Happy to share the final version of this work is now out in @natchembio.nature.com. Lots of additional exciting data! Congrats to all the authors!

Posttranslational modifications remodel proteome-wide ligandability - Nature Chemical Biology

A chemoproteomic strategy reveals how posttranslational modifications reshape protein ligandability across the human proteome, uncovering more than 400 state-dependent interactions, including phosphor...

nature.com

Chris Parker@chrisgparker.bsky.social · last yr.

Excited to share a new preprint from the lab. We show that PTMs like phosphorylation & glycosylation dynamically reshape proteome-wide ligandability in cells, including proteins like KRAS. Great collaboration with the Huang Lab, @forlilab.bsky.social and BMS. www.biorxiv.org/content/10.1...

Really fun and challenging (!) discussion with @cdbahl.com on BindCraft, the state of binder design, the oustanding challenges and perhaps also some misconceptions in the field 💫 www.healthtech.com/the-chain/ma...

Episode 84 Martin Pacesa on BindCraft An Automated Pipeline for De Novo Protein Binder Design

April 14, 2026 | How is BindCraft, the automated pipeline for de novo protein binder design, changing the protein design industry? Martin Pacesa, assistant professor of pharmacology at the University ...

healthtech.com

We just passed an exciting milestone: our one thousandth member just joined @bpdmc.org! Thank you so much to everyone who has made this journey possible, and we're excited to welcome many more wonderful folks to our nerdy protein club! For more info, check out bpdmc.org

Quick reminder to join us at @danafarber.bsky.social tonight for a great talk by Isaac Lutz!

Boston Protein Design and Modeling Club@bpdmc.org · 4mo ago

No joke, we've got an exciting seminar this month from Isaac Lutz Wednesday, April 8th 2026 at 7pm EDT in Room 6055, Longwood Center, @danafarber.bsky.social "Creativity at Scale: Problem Formulation as the Frontier of Protein Design" bpdmc.org

Here is the talk I gave @asbmb.bsky.social for the DeLano Award in Computational Biosciences in March 2026. www.youtube.com/watch?v=g0Gv...

Roland Dunbrack: Structural bioinformatics and protein structure prediction at multiple scales

YouTube video by American Society for Biochemistry and Molecular Biology (ASBMB)

youtube.com

No joke, we've got an exciting seminar this month from Isaac Lutz Wednesday, April 8th 2026 at 7pm EDT in Room 6055, Longwood Center, @danafarber.bsky.social "Creativity at Scale: Problem Formulation as the Frontier of Protein Design" bpdmc.org

schedule

introduction and membership Boston Protein Design and Modeling Club (BPDMC) is a community of computational protein engineers and modelers from both academia and industry. While we are based in Boston...

bpdmc.org

Only 2 weeks left to benefit from early-bird registration rate! The 6th Protein Engineering Canada Conference will be held on June 22-24 in Ottawa, Canada. More information here: event.fourwaves.com/pec2026/pages

6th Protein Engineering Canada (PEC) Conference

Join 6th Protein Engineering Canada (PEC) Conference, June 22-24, 2026. Learn more on Fourwaves.

event.fourwaves.com

New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9