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Boston Protein Design and Modeling Club @bpdmc.org · 7d

quick reminder to join us at @danafarber.bsky.social tonight for a spectacular seminar by @marinkazitnik.bsky.social!

Boston Protein Design and Modeling Club @bpdmc.org · 12d

Our September seminar was delayed a couple weeks, but our speaker @marinkazitnik.bsky.social is well worth the wait.

Join us this Wednesday, October 1st 2025 at 7pm EDT in Room 6055, Longwood Center, @danafarber.bsky.social

"Empowering Biomedical Discovery with AI Scientists”

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

1 1

Boston Protein Design and Modeling Club @bpdmc.org · 12d

Our September seminar was delayed a couple weeks, but our speaker @marinkazitnik.bsky.social is well worth the wait.

Join us this Wednesday, October 1st 2025 at 7pm EDT in Room 6055, Longwood Center, @danafarber.bsky.social

"Empowering Biomedical Discovery with AI Scientists”

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

1 1

Boston Protein Design and Modeling Club @bpdmc.org · 29d

If you missed seeing @colby.tuple.xyz's excellent talk back in July, you can now check out the recording 👇 youtu.be/k63Xh-oJMs0

Model. Package. Deploy. Repeat: A DevOps Approach to Biomolecular Scalability

YouTube video by Boston Protein Design and Modeling Club

youtu.be

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Boston Protein Design and Modeling Club @bpdmc.org · Aug 15

Have no fear if you weren't in the packed audience this week for @martinpacesa.bsky.social's awesome seminar, because you can check out the recording 👇
youtu.be/qQihl6If9vU

BindCraft: one-shot design of functional protein binders

YouTube video by Boston Protein Design and Modeling Club

youtu.be

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Boston Protein Design and Modeling Club @bpdmc.org · Aug 13

Fun fact: #bindcraft evolved from a binder design tutorial originally developed for BPDMC!

Come see @martinpacesa.bsky.social tonight at 7pm EDT in Room 181, Building 68, @mit.edu

"BindCraft: one-shot design of functional protein binders"

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

4 10

Boston Protein Design and Modeling Club @bpdmc.org · Jul 9

quick reminder to join us tonight at @harvardmed.bsky.social for a great talk by Colby Ford @colby.tuple.xyz

Boston Protein Design and Modeling Club @bpdmc.org · Jul 2

Come learn about how to run the computational infrastructure that's powering the protein design revolution

July 9th 2025 at 7pm EDT in TMEC250 @harvardmed.bsky.social

"Model. Package. Deploy. Repeat: A DevOps Approach to Biomolecular Scalability"

Colby Ford @colby.tuple.xyz

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

3 2

Boston Protein Design and Modeling Club @bpdmc.org · Jul 2

Come learn about how to run the computational infrastructure that's powering the protein design revolution

July 9th 2025 at 7pm EDT in TMEC250 @harvardmed.bsky.social

"Model. Package. Deploy. Repeat: A DevOps Approach to Biomolecular Scalability"

Colby Ford @colby.tuple.xyz

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

1 5

Boston Protein Design and Modeling Club @bpdmc.org · Jun 12

Don't fret if you missed Silvi Rouskin's brilliant and engaging talk on #RNA structure last night - you can check out the recording 👇
youtu.be/oS_Cb-YMymw

RNA Function, Design, and Modeling

YouTube video by Boston Protein Design and Modeling Club

youtu.be

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Boston Protein Design and Modeling Club @bpdmc.org · Jun 5

Protein isn't the only amazing macromolecule that folds into 3D shapes - come see Silvi Rouskin in Room 181, Building 68 at MIT on Wednesday, June 11th at 7pm EDT to learn more about #RNA structure design and modeling!

"RNA Function, Design, and Modeling"

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

1 9

Boston Protein Design and Modeling Club @bpdmc.org · May 16

If you missed out on Sarel Fleishman's extraordinary talk last night, have no fear - you can check out the recording 👇
youtu.be/2aaWh8yVq8U

Designing new and improved functions in natural protein folds

YouTube video by Boston Protein Design and Modeling Club

youtu.be

1 11

Boston Protein Design and Modeling Club @bpdmc.org · May 15

quick reminder to come join us tonight at 7pm EDT to see Sarel Fleishman!

Boston Protein Design and Modeling Club @bpdmc.org · May 9

Our speaker next week is an amazing scientist from out of town, and this is one that you won't want to miss!

Thursday, May 15th, 7pm EDT
Cannon Room, Building C, @harvardmed.bsky.social

Sarel Fleishman
www.fleishmanlab.org

"Designing new and improved functions in natural protein folds"

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

1 2

Boston Protein Design and Modeling Club @bpdmc.org · May 9

and please note the change in date!

Boston Protein Design and Modeling Club @bpdmc.org · May 9

Our speaker next week is an amazing scientist from out of town, and this is one that you won't want to miss!

Thursday, May 15th, 7pm EDT
Cannon Room, Building C, @harvardmed.bsky.social

Sarel Fleishman
www.fleishmanlab.org

"Designing new and improved functions in natural protein folds"

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

1 2 4

Boston Protein Design and Modeling Club @bpdmc.org · May 3

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...

Design of small molecule binding proteins using deep learning

YouTube video by Boston Protein Design and Modeling Club

youtu.be

3 2

Reposted by Boston Protein Design and Modeling Club

Nick Polizzi @nickpolizzi.bsky.social · Apr 28

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...
🧵🧪

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

Computational design of molecular recognition remains challenging despite advances in deep learning. The design of proteins that bind to small molecules has been particularly difficult because it requ...

www.biorxiv.org

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Boston Protein Design and Modeling Club @bpdmc.org · Apr 18

If you missed @lindseyguan.bsky.social's outstanding talk last week, you can check out the recording 👇
youtu.be/R87pmoB3QF0

Interpreting state-of-the-art structure predictors for protein-peptide complexes

YouTube video by Boston Protein Design and Modeling Club

youtu.be

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Boston Protein Design and Modeling Club @bpdmc.org · Apr 7

Yes, there is a live stream option, and we share the zoom link with BPDMC members. You can find instructions for how to sign up at 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

Boston Protein Design and Modeling Club @bpdmc.org · Apr 5

We're so excited - our upcoming seminar will be by Lindsey Guan on Wednesday, April 9th 2025 starting at 7pm EDT in Room 181, Building 68, MIT @mitofficial.bsky.social

"Interpreting state-of-the-art structure predictors for protein-peptide complexes"

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

1 5

Boston Protein Design and Modeling Club @bpdmc.org · Mar 13

if you missed seeing Seth Fraden's great seminar last night, have no fear - you can check out the recording: youtu.be/zyJmWLzkh7Q

From DNA Origami to Protein Design: Symmetry-Guided Principles Across Scales

YouTube video by Boston Protein Design and Modeling Club

youtu.be

1 6

Boston Protein Design and Modeling Club @bpdmc.org · Mar 12

quick reminder - don't miss out on an awesome seminar by Seth Fraden tonight!

Boston Protein Design and Modeling Club @bpdmc.org · Mar 6

As usual, we've got another exciting seminar coming up!

Come see Seth Fraden on Wednesday, March 12th 2025 at 7pm EDT in the Cannon Room, Building C, Harvard Medical School

"From DNA Origami to Protein Design: Symmetry-Guided Principles Across Scales"

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

Reposted by Boston Protein Design and Modeling Club

OMSF @omsf.io · Mar 10

@bpdmc.bsky.social hosts those on the bleeding edge of molecular modeling. if you want to know what's what, check out their YouTube page. here's the latest presentation:

Boltz-1 and the Future of Biomolecular Foundation Models

YouTube video by Boston Protein Design and Modeling Club

www.youtube.com

1 2

Boston Protein Design and Modeling Club @bpdmc.org · Mar 6

As usual, we've got another exciting seminar coming up!

Come see Seth Fraden on Wednesday, March 12th 2025 at 7pm EDT in the Cannon Room, Building C, Harvard Medical School

"From DNA Origami to Protein Design: Symmetry-Guided Principles Across Scales"

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

2

Boston Protein Design and Modeling Club @bpdmc.org · Feb 25

for the folks who missed seeing @gcorso.bsky.social and @jeremywohlwend.bsky.social give their awesome seminar live the other week, you can check out the recording 👇
youtu.be/K-gzTJMy1ag

Boltz-1 and the Future of Biomolecular Foundation Models

YouTube video by Boston Protein Design and Modeling Club

youtu.be

1 11

Boston Protein Design and Modeling Club @bpdmc.org · Feb 10

We've got an exciting seminar by @gcorso.bsky.social and @jeremywohlwend.bsky.social coming up this Wednesday, February 12th starting at 7pm EST in Room 181, Building 68, MIT

"Towards a Unified Approach for Biomolecular Interaction Modeling: Boltz-1 and the Future of Biomolecular Foundation Models"

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Boston Protein Design and Modeling Club @bpdmc.org · Jan 15

quick reminder to come join us in the Cannon Room tonight (which is not yet under construction) to see a great seminar by Ben Fry!

Boston Protein Design and Modeling Club @bpdmc.org · Jan 6

We can't wait for Ben Fry to kick off our 2025 seminar series next week. Come join us on Wednesday, January 15th at 7pm EST in the Cannon Room, @harvardmed.bsky.social

"Design of small molecule binding proteins using deep learning"

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