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Boston Protein Design and Modeling Club @bpdmc.org · 8h

quick reminder to join us at DFCI tonight to see Chris Norn!

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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026

ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...

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Chris Bahl @cdbahl.com · 18/09/2026

We always strive for our work to substantially benefit the greater scientific community, and it's such a thrill every time it happens. A massive thank you to @addgene.bsky.social for amplifying the impact of researchers everywhere! 🧵👇

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Boston Protein Design and Modeling Club @bpdmc.org · 18/09/2026

If you missed @jeffreyjgray.bsky.social's wicked awesome seminar back in February where he presented a ton of unpublished data, don't worry because you can finally get all caught up 👇 youtu.be/hJqgu2amqI0

youtu.be

Antibody language models vs. biology; protein docking denoising diffusion models vs. physics

YouTube video by Boston Protein Design and Modeling Club

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Boston Protein Design and Modeling Club @bpdmc.org · 09/09/2026

Quick reminder to join us at MIT tonight to see Natasha Murakowska give a great talk!

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Protein Society @proteinsociety.bsky.social · 04/09/2026

🧬 Figure Friday AI is making protein design faster, but can protein production keep up? Edson Noriega, Chris Bahl & colleagues developed a high-throughput workflow for rapid protein purification, demonstrated across 96 diverse proteins.

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Boston Protein Design and Modeling Club @bpdmc.org · 02/09/2026

Come join us on Wednesday, September 9th 2026 at 7pm EDT in Room 181, Building 68, @mit.edu to see Natasha Murakowska! "Quantitative Affinity Data at Scale: Addressing the Data Bottleneck in AI-Enabled Protein Design"

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Rosetta Commons @rosettacommons.bsky.social · 18/08/2026

🧬 Want to stay updated on protein science? Check out the @bpdmc.org monthly presentation series! Recent topics: • Computational antibody design • Energy-based models & structure • De novo small-molecule induced changes Learn more, watch past presentations, and join the community at bpdmc.org.

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Boston Protein Design and Modeling Club @bpdmc.org · 14/08/2026

If you weren't able to make it out for Jeffrey Chang's marvelous seminar this week, you can check out the recording 👇 youtu.be/q3Xn2-TIZEo

youtu.be

De novo design of small-molecule-induced conformational change

YouTube video by Boston Protein Design and Modeling Club

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Boston Protein Design and Modeling Club @bpdmc.org · 12/08/2026

Quick reminder to join us tonight at DCFI for a super exciting talk by Jeffrey Chang!

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Nick Polizzi @nickpolizzi.bsky.social · 12/08/2026

Happening tonight! Come join in person or on zoom to hear Jeffrey talk about his work. Questions from zoom audience encouraged! www.bpdmc.org/schedule

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...

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Chris Bahl @cdbahl.com · 05/08/2026

The data, code, and detailed protocols are all available on github github.com/aiproteins/h... and all the plasmids are available on addgene www.addgene.org/233685/ www.addgene.org/233686/ www.addgene.org/kits/bahl-su...

github.com

GitHub - aiproteins/high_throughput_protein_production

Contribute to aiproteins/high_throughput_protein_production development by creating an account on GitHub.

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Chris Bahl @cdbahl.com · 05/08/2026

Every protein designer knows that producing & testing designed proteins is a foundational capability for our field, & this is still pretty challenging for a lot of folks. This is why I'm delighted to share our work to make high-throughput protein production more accessible dx.doi.org/10.1002/pro....

dx.doi.org

Facile, high‐throughput protein purification enabled by high‐efficiency protease elution

While advances in artificial intelligence have made protein design widely accessible, protein production and characterization remain a bottleneck. Protease-cleavable affinity tags are commonly used t....

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Nick Polizzi @nickpolizzi.bsky.social · 05/08/2026

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. 🧵

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Boston Protein Design and Modeling Club @bpdmc.org · 05/08/2026

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"

biorxiv.org

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...

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Boston Protein Design and Modeling Club @bpdmc.org · 09/07/2026

If you missed James Roney's stellar talk last night, have no fear because you can check out the recording 👇 youtu.be/oZZumtlUXag

youtu.be

Energy-Based Models of Protein Structure, Dynamics, and Folding

YouTube video by Boston Protein Design and Modeling Club

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Boston Protein Design and Modeling Club @bpdmc.org · 08/07/2026

quick reminder to join us at @mit.edu tonight for an awesome talk by James Roney from @sokrypton.org's lab!

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Boston Protein Design and Modeling Club @bpdmc.org · 06/07/2026

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

bpdmc.org

schedule

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Boston Protein Design and Modeling Club @bpdmc.org · 02/07/2026

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

youtu.be

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

YouTube video by Boston Protein Design and Modeling Club

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AI Proteins @aiproteins.com · 25/06/2026

Three weeks ago, we welcomed the local scientific community to join us at our headquarters in Kenmore Square for the inaugural lecture in the AI Proteins Seminar Series. Our speaker Neil King from @uwproteindesign.bsky.social delivered a superb seminar. Check it out 👇 youtu.be/OPRMfRnlx1k

youtu.be

Neil King: ML-based design of nanoparticle vaccines (AI Proteins Seminar Series)

YouTube video by AI Proteins

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Boston Protein Design and Modeling Club @bpdmc.org · 10/06/2026

quick reminder to head over to @mit.edu tonight for a great seminar!

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Boston Protein Design and Modeling Club @bpdmc.org · 08/06/2026

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

bpdmc.org

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Protein Society @proteinsociety.bsky.social · 03/06/2026

⏰ Tomorrow! Join our webinar, Introduction to Protein Design for Africa, featuring speakers from AI Proteins, STEAMulater, Minimal Bio, and Nostrum Biodiscovery. Learn how protein design is advancing innovation and accessibility around the world! Register: us06web.zoom.us/webinar/regi...

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AI Proteins @aiproteins.com · 03/06/2026

Thank you to everyone who attended the inaugural lecture in the AI Proteins Seminar Series today. Neil King @kinglabipd.bsky.social gave a fantastic talk to a packed house!

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AI Proteins @aiproteins.com · 01/06/2026

We're delighted to kick off our new seminar series, and the inaugural speaker is none other than Neil King from the Institute for Protein Design, University of Washington "ML-based design of nanoparticle vaccines" June 3rd, 2026 12:00 PM – 1:00 PM EDT

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Boston Protein Design and Modeling Club @bpdmc.org · 15/05/2026

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

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Boston Protein Design and Modeling Club @bpdmc.org · 06/05/2026

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

bpdmc.org

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Rosetta Commons @rosettacommons.bsky.social · 06/05/2026

Prof. Frank Noé is a leading figure at the intersection of machine learning and molecular science, with pioneering contributions that are reshaping our field. Hear his perspective at European RosettaCon 2026. Early bird registration closes May 31. europeanrosettacon.org

An announcement of Frank Noé as a keynote speaker for European RosettaCon. It notes he is from Freie Universität Berlin and Microsoft Research AI for Science and his talk will be titled Biomolecular dynamics and function at scale. At the bottom are the logos for NOVA University, SPBf, Rosetta Commons, and Rosetta Design Group. The background has a purple colored sky at the top and then an off-white background for most of the image with some purple spirals on the sides.

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Martin Pacesa @martinpacesa.bsky.social · 14/04/2026

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...

healthtech.com

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 ...

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Boston Protein Design and Modeling Club @bpdmc.org · 10/04/2026

If you missed Isaac Lutz's awesome seminar this week where he showcased state-of-the-art protein design starting from the days of physics-based energy functions all the way to modern agentic workflows, then you'll definitely want to check out the recording 👇 youtu.be/rSfSWc9wdDg

youtu.be

Creativity at Scale: Problem Formulation as the Frontier of Protein Design

YouTube video by Boston Protein Design and Modeling Club

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Boston Protein Design and Modeling Club @bpdmc.org · 09/04/2026

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

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Boston Protein Design and Modeling Club @bpdmc.org · 08/04/2026

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

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Boston Protein Design and Modeling Club @bpdmc.org · 01/04/2026

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

bpdmc.org

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Rosetta Commons @rosettacommons.bsky.social · 31/03/2026

Today is the last day to register for Summer RosettaCon 2026 at the early bird rate. We hope you’ll join us in Seattle, WA as we gather and discuss this year’s theme, “Biomolecule Engineering: From Principle to Practice.” Register today! rosettacon.org

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Chris Bahl @cdbahl.com · 31/03/2026

We've got two more positions open for RAs to join AI Proteins! One opening is for our Protein Characterization group led by Alyssa Anderson, and the other is for our Biochemistry group led by Edson Carcamo. These wet lab roles are a perfect for college students who are graduating this spring.

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Boston Protein Design and Modeling Club @bpdmc.org · 11/03/2026

Quick reminder to join us at @danafarber.bsky.social tonight for an awesome talk by Jody Mou!

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Chris Bahl @cdbahl.com · 09/03/2026

We're recruiting a Research Associate to join our Bioprocess Development team. This is a wet lab role ideally suited for someone graduating college this spring who is excited to join a team pioneering a new therapeutic modality Check it out! 👇 www.aiproteins.com/open-positio...

aiproteins.com

Research Associate in Bioprocess Development | AI Proteins

Mar 06, 2026

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Boston Protein Design and Modeling Club @bpdmc.org · 05/03/2026

Spring is arriving in Boston and Jody Mou linkedin.com/in/jody-mou has some fresh new data to share! Wednesday, March 11th 2026, 7pm EDT in Room 6055, Longwood Center @danafarber.bsky.social "Computational Design of a Rapid and Orthogonal Self-Labeling Protein Tag for Live-Cell Imaging" bpdmc.org

bpdmc.org

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Jeffrey J. Gray @jeffreyjgray.bsky.social · 02/03/2026

Enjoying a swing through New England. After a fun time at @bpdmc.org, Ethan Eschbach hosted me for a visit with @sandercbio.bsky.social and the @deboramarks.bsky.social lab. I was also thrilled to give a talk at the Thayer School of Engineering at Dartmouth hosted by T. Emme Burgin. What a fun week!

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Boston Protein Design and Modeling Club @bpdmc.org · 26/02/2026

A huge thanks to everyone who packed the house at @mit.edu last night for a rockstar talk by @jeffreyjgray.bsky.social!

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Boston Protein Design and Modeling Club @bpdmc.org · 25/02/2026

Quick reminder to join us at MIT tonight because Jeff Gray is speaking!

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Nick Polizzi @nickpolizzi.bsky.social · 20/02/2026

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.

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Boston Protein Design and Modeling Club @bpdmc.org · 21/02/2026

We've got Jeff Gray (graylab.jhu.edu) coming to present this month!! Wednesday, February 25th 2026, starting at 7pm EST in Room 181, Building 68, @MIT "Antibody language models vs. biology; protein docking denoising diffusion models vs. physics" bpdmc.org

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Boston Protein Design and Modeling Club @bpdmc.org · 23/01/2026

Don't worry if you missed the excellent seminar by Mike Nichols and Erik Swanson from @manifoldbio.bsky.social this week because you can check out the recording 👇 youtu.be/u9dznMvcDs4

youtu.be

mBER: Controllable de novo antibody design with million-scale experimental screening

YouTube video by Boston Protein Design and Modeling Club

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Boston Protein Design and Modeling Club @bpdmc.org · 21/01/2026

quick reminder to join us at @mit.edu tonight for our first meeting of 2026!

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Boston Protein Design and Modeling Club @bpdmc.org · 03/01/2026

Happy New Year! We've got an exciting seminar to kick off 2026 Wednesday, January 21st at 7pm EST Room 181, Building 68 @mit.edu speaker: Erik Swanson and Mike Nichols "mBER: Controllable de novo antibody design with million-scale experimental screening" bpdmc.org

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Boston Protein Design and Modeling Club @bpdmc.org · 11/12/2025

If you couldn't make it for @yehlincho.bsky.social's rockstar seminar last night, have no fear because you can check out the recording 👇 youtu.be/yCOlC_yj4kc

youtu.be

How AF3-Style Structure Prediction Models Can Be Used for Design: BoltzDesign and Protein Hunter

YouTube video by Boston Protein Design and Modeling Club

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