Boston Protein Design and Modeling Club
@bpdmc.org
We are a global community of computational protein engineers and modelers from both academia and industry.
An @omsf.io project organized by @cdbahl.com, @sokrypton.org, and @nickpolizzi.bsky.social
https://bpdmc.org
An @omsf.io project organized by @cdbahl.com, @sokrypton.org, and @nickpolizzi.bsky.social
https://bpdmc.org
If you missed Jody Mou's terrific seminar back in March where she presented a bunch of unpublished data from her work in @nickpolizzi.bsky.social's lab, you can finally get all caught up 👇
youtu.be/SdkBhhBWZWk
and pre-print: doi.org/10.64898/202...
youtu.be/SdkBhhBWZWk
and pre-print: doi.org/10.64898/202...
Computational Design of a Rapid and Orthogonal Self-Labeling Protein Tag for Live-Cell Imaging
YouTube video by Boston Protein Design and Modeling Club
youtu.be
October 7, 2026 at 11:05 PM
If you missed Jody Mou's terrific seminar back in March where she presented a bunch of unpublished data from her work in @nickpolizzi.bsky.social's lab, you can finally get all caught up 👇
youtu.be/SdkBhhBWZWk
and pre-print: doi.org/10.64898/202...
youtu.be/SdkBhhBWZWk
and pre-print: doi.org/10.64898/202...
If you missed the superb lecture last week by Chris Norn, have no fear because you can check out the recording 👇
youtu.be/czkQXg0wwrw
youtu.be/czkQXg0wwrw
De novo design of miniproteins targeting GPCRs
YouTube video by Boston Protein Design and Modeling Club
youtu.be
October 6, 2026 at 1:22 PM
If you missed the superb lecture last week by Chris Norn, have no fear because you can check out the recording 👇
youtu.be/czkQXg0wwrw
youtu.be/czkQXg0wwrw
Reposted by Boston Protein Design and Modeling Club
Researchers from @aiproteins.com introduce a streamlined workflow that could reshape how labs produce proteins at scale. The method tackles key bottlenecks across the entire protein production pipeline and is designed to be fully compatible with automation.
Read more: zurl.co/kAHMW
Read more: zurl.co/kAHMW
October 5, 2026 at 4:30 PM
Researchers from @aiproteins.com introduce a streamlined workflow that could reshape how labs produce proteins at scale. The method tackles key bottlenecks across the entire protein production pipeline and is designed to be fully compatible with automation.
Read more: zurl.co/kAHMW
Read more: zurl.co/kAHMW
quick reminder to join us at DFCI tonight to see Chris Norn!
We moved our next meeting up by 2 weeks so Chris Norn can come present while he's in town! Join us on Wednesday, September 30th 2026 at 7pm EDT in Room 6055, Longwood Center, @danafarber.bsky.social
"De novo design of miniproteins targeting GPCRs"
bpdmc.org
"De novo design of miniproteins targeting GPCRs"
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 USA, BPDMC is also a global online community open to everyone. Please send us an email and
bpdmc.org
September 30, 2026 at 1:34 PM
quick reminder to join us at DFCI tonight to see Chris Norn!
If you missed Natasha Murakowska's really great seminar the other week, don't fret as you can check out the recording 👇
youtu.be/tjAPYPpQylo
youtu.be/tjAPYPpQylo
Quantitative Affinity Data at Scale: Addressing the Data Bottleneck in AI-Enabled Protein Design
YouTube video by Boston Protein Design and Modeling Club
youtu.be
September 22, 2026 at 12:50 PM
If you missed Natasha Murakowska's really great seminar the other week, don't fret as you can check out the recording 👇
youtu.be/tjAPYPpQylo
youtu.be/tjAPYPpQylo
Reposted by Boston Protein Design and Modeling Club
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...
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...
September 21, 2026 at 9:55 AM
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...
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...
We moved our next meeting up by 2 weeks so Chris Norn can come present while he's in town! Join us on Wednesday, September 30th 2026 at 7pm EDT in Room 6055, Longwood Center, @danafarber.bsky.social
"De novo design of miniproteins targeting GPCRs"
bpdmc.org
"De novo design of miniproteins targeting GPCRs"
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 USA, BPDMC is also a global online community open to everyone. Please send us an email and
bpdmc.org
September 21, 2026 at 5:46 PM
We moved our next meeting up by 2 weeks so Chris Norn can come present while he's in town! Join us on Wednesday, September 30th 2026 at 7pm EDT in Room 6055, Longwood Center, @danafarber.bsky.social
"De novo design of miniproteins targeting GPCRs"
bpdmc.org
"De novo design of miniproteins targeting GPCRs"
bpdmc.org
Reposted by Boston Protein Design and Modeling Club
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!
🧵👇
🧵👇
September 18, 2026 at 5:31 PM
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!
🧵👇
🧵👇
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/hJqgu2amqI0
Antibody language models vs. biology; protein docking denoising diffusion models vs. physics
YouTube video by Boston Protein Design and Modeling Club
youtu.be
September 18, 2026 at 3:07 PM
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/hJqgu2amqI0
Quick reminder to join us at MIT tonight to see Natasha Murakowska give a great talk!
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"
"Quantitative Affinity Data at Scale: Addressing the Data Bottleneck in AI-Enabled Protein Design"
September 9, 2026 at 1:48 PM
Quick reminder to join us at MIT tonight to see Natasha Murakowska give a great talk!
Reposted by Boston Protein Design and Modeling Club
🧬 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.
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.
September 4, 2026 at 6:24 PM
🧬 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.
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.
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"
"Quantitative Affinity Data at Scale: Addressing the Data Bottleneck in AI-Enabled Protein Design"
September 2, 2026 at 10:09 PM
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"
"Quantitative Affinity Data at Scale: Addressing the Data Bottleneck in AI-Enabled Protein Design"
Reposted by Boston Protein Design and Modeling Club
🧬 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.
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.
August 18, 2026 at 2:29 PM
🧬 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.
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.
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/q3Xn2-TIZEo
De novo design of small-molecule-induced conformational change
YouTube video by Boston Protein Design and Modeling Club
youtu.be
August 14, 2026 at 3:46 PM
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/q3Xn2-TIZEo
Quick reminder to join us tonight at DCFI for a super exciting talk by Jeffrey Chang!
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"
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...
www.biorxiv.org
August 12, 2026 at 6:55 PM
Quick reminder to join us tonight at DCFI for a super exciting talk by Jeffrey Chang!
Reposted by Boston Protein Design and Modeling Club
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
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...
www.bpdmc.org
August 12, 2026 at 4:42 PM
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
Reposted by Boston Protein Design and Modeling Club
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/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 - aiproteins/high_throughput_protein_production
Contribute to aiproteins/high_throughput_protein_production development by creating an account on GitHub.
github.com
August 5, 2026 at 7:08 PM
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/aiproteins/h...
and all the plasmids are available on addgene
www.addgene.org/233685/
www.addgene.org/233686/
www.addgene.org/kits/bahl-su...
Reposted by Boston Protein Design and Modeling Club
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/10.1002/pro....
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....
dx.doi.org
August 5, 2026 at 6:57 PM
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/10.1002/pro....
Reposted by Boston Protein Design and Modeling Club
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. 🧵
August 5, 2026 at 12:18 AM
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. 🧵
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"
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...
www.biorxiv.org
August 4, 2026 at 11:37 PM
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"
Wednesday, August 12th 2026, 7pm EDT in Room 6055, Longwood Center, @danafarber.bsky.social
"De novo design of small-molecule-induced conformational change"
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/oZZumtlUXag
Energy-Based Models of Protein Structure, Dynamics, and Folding
YouTube video by Boston Protein Design and Modeling Club
youtu.be
July 9, 2026 at 7:21 PM
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/oZZumtlUXag
quick reminder to join us at @mit.edu tonight for an awesome talk by James Roney from @sokrypton.org's lab!
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
"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
July 8, 2026 at 2:23 PM
quick reminder to join us at @mit.edu tonight for an awesome talk by James Roney from @sokrypton.org's lab!
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
"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
July 6, 2026 at 10:24 PM
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
"Energy-Based Models of Protein Structure, Dynamics, and Folding"
bpdmc.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
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
July 2, 2026 at 5:53 PM
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/w-NddBw2FJk
Reposted by Boston Protein Design and Modeling Club
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/OPRMfRnlx1k
Neil King: ML-based design of nanoparticle vaccines (AI Proteins Seminar Series)
YouTube video by AI Proteins
youtu.be
June 25, 2026 at 6:55 PM
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/OPRMfRnlx1k