Nick Polizzi

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...

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

GitHub - polizzilab/LASErMPNN: All-Atom (Including Hydrogen!) Ligand-Conditioned Protein Sequence Design & Sidechain Packing GNN All-Atom (Including Hydrogen!) Ligand-Conditioned Protein Sequence Design & Sidechain Packing GNN - polizzilab/LASErMPNN

New Title Alert: LASErMPNN- is an all-atom ligand-conditioned protein sequence design and sidechain packing model that accounts for the presence of small molecules, including hydrogens.

Learn more here: buff.ly/cZcOmpC

#SBGridSoftware #SBGrid #StructuralBiology

Would ideally be a 2 yr commitment. I’ll update this thread with an official link to submit an application (coming soon), but in the meantime please feel free to email me with a CV and cover letter!

The tech would focus on protein-ligand binding, getting experience with biophysical methods such as SPR, ITC, fluorescence spectroscopy, NMR, X-ray crystallography, etc. Would also get experience with computational protein-design tools (though the role is primarily focused on experiments).

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.

Principles of in situ protein sequencing: expansion microscopy-adapted Edman degradation and amino acid recognition https://www.biorxiv.org/content/10.64898/2026.01.29.702630v1

Read the Save HHS open letter!

www.savehhs.org/letter-we-wi...

Now hiring: Tenure-track faculty (Asst/Assoc/Full) in Computational & Experimental Protein Design at Fox Chase Cancer Center, Philadelphia PA   Join the Cancer Signaling & Microenvironment Pro... Now hiring: Tenure-track faculty (Asst/Assoc/Full) in Computational & Experimental Protein Design at Fox Chase Cancer Center, Philadelphia PA   Join the Cancer Signaling & Microenvironment Program at ...

The Cancer Signaling & Microenvironment Program at Fox Chase Cancer Center is looking for tenure track faculty (assist./assoc./full) in computational & experimental protein design. CV & 3-page research statement by Feb 15.

More info here:
www.linkedin.com/feed/update/...

Questions: DM/Email me.

Exciting stuff, Gabriele. Congrats!

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...

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

Large scale prospective evaluation of co-folding across 557 Mac1-ligand complexes and three virtual screens https://www.biorxiv.org/content/10.64898/2025.12.25.696505v1

As someone trained in physics, this project really helped me learn the nuances of denoising diffusion models. The “time” variable acts as an alchemical transformation—e.g. RFDiffusion transforms between protein structure and an ideal gas.

Read the paper here!
www.biorxiv.org/content/10.1...

YouTube video by Boston Protein Design and Modeling Club How AF3-Style Structure Prediction Models Can Be Used for Design: BoltzDesign and Protein Hunter

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

quick reminder to join us tonight for our final meeting of 2025 - it's going to be a great seminar by @yehlincho.bsky.social that you won't want to miss!

Announcement for the 6th Protein Engineering Canada Conference, to be held June 22nd-24th in Ottawa, Canada. The image shows a protein structure in front of a picture of Parliament Hill and Chateau Laurier in Ottawa.

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Save the date!

The 6th Protein Engineering Canada Conference will be held on June 22-24 in Ottawa, Canada.

Abstract submission and registration are open!

More information here: event.fourwaves.com/pec2026/pages

Crystallographic Ensembles Reveal the Structural Basis of Binding Entropy in SARS-CoV2 Macrodomain Structure-based drug design has traditionally focused on optimizing static, enthalpic interactions between ligands and proteins or on displacing binding site solvent molecules to entropically favor bi...

New preprint! Entropy drives molecular recognition, yet most structure-based drug design ignores it because it is difficult to measure. X-ray crystallography captures ensembles, not single structures. Can we extract thermodynamically meaningful entropy from them?

www.biorxiv.org/content/10.1...

YouTube video by Boston Protein Design and Modeling Club Learning millisecond protein dynamics from what is missing in NMR spectra

Don't fret if you weren't in the room this week when @ginaelnesr.bsky.social gave her stellar seminar because you can check out the recording 👇
youtu.be/I-utRMS84E8

Congrats, Gabe! Interesting re: arg. Mutating surface lys —> arg also is known to help w crystallization. Wonder if related 🤔

Congrats, Chris!

Google Colab

@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...

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...

We can't wait until Wednesday, November 19th 2025 to arrive because we have @ginaelnesr.bsky.social from @possuhuanglab.bsky.social speaking at 7pm EST in Room 6055, Longwood Center, @danafarber.bsky.social

"Learning millisecond protein dynamics from what is missing in NMR spectra"

bpdmc.org

Heartbreaking. So sorry to hear this, Willow

Last week to apply!

thanks everyone who packed the house tonight at @mit.edu for an incredible seminar by @grocklin.bsky.social!

quick reminder to come see @grocklin.bsky.social tonight at @mit.edu!

Economic Budgeting for Endowment-Dependent Universities Founded in 1920, the NBER is a private, non-profit, non-partisan organization dedicated to conducting economic research and to disseminating research findings among academics, public policy makers, an...

If you wonder why doesn't Harvard use its endowment: the answer, of course, is that we do. A major source of Harvard's annual budget is the endowment investment return.

For anyone seriously interested in how university endowments work, an excellent wonky reference:

www.nber.org/papers/w32506

Training bias and sequence alignments shape protein–peptide docking by AlphaFold and related methods Protein-peptide interactions mediate many biological processes. Accurate structural models of protein-peptide complexes, determined by experiment or computational prediction, are essential for unders...

now out in Protein Science! onlinelibrary.wiley.com/doi/10.1002/...

Excited to share our new preprint “Unified Sampling and Ranking for Protein Docking with DFMDock” by PhD candidate Lee-Shin Chu and Post-Doc Sudeep Sarma! We designed a diffusion docking model that samples rigid-body conformations by predicting forces and ranks poses using predicted energies.

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

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...

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