Nick Polizzi
@nickpolizzi.bsky.social
Asst prof at HMS, PI at DFCI
Designing proteins
polizzilab.org
Designing proteins
polizzilab.org
Reposted by Nick Polizzi
Reposted by Nick Polizzi
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.
More info here:
www.linkedin.com/feed/update/...
Questions: DM/Email me.
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 ...
www.linkedin.com
January 19, 2026 at 3:57 AM
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.
More info here:
www.linkedin.com/feed/update/...
Questions: DM/Email me.
Reposted by Nick Polizzi
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
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
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
January 3, 2026 at 3:59 PM
Reposted by Nick Polizzi
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
December 29, 2025 at 1:46 AM
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
Reposted by Nick Polizzi
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...
Read the paper here!
www.biorxiv.org/content/10.1...
December 23, 2025 at 7:18 PM
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...
Read the paper here!
www.biorxiv.org/content/10.1...
Reposted by Nick Polizzi
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/yCOlC_yj4kc
How AF3-Style Structure Prediction Models Can Be Used for Design: BoltzDesign and Protein Hunter
YouTube video by Boston Protein Design and Modeling Club
youtu.be
December 11, 2025 at 2:13 PM
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/yCOlC_yj4kc
Reposted by Nick Polizzi
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!
Join us Wednesday December 10th for an amazing seminar by @yehlincho.bsky.social to cap off 2025. See you at 7pm EST in Room 6055, Longwood Center @danafarber.bsky.social
"How AF3-Style Structure Prediction Models Can Be Used for Protein Design: BoltzDesign and Protein Hunter"
bpdmc.org
"How AF3-Style Structure Prediction Models Can Be Used for Protein Design: BoltzDesign and Protein Hunter"
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
December 10, 2025 at 3:29 PM
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!
Reposted by Nick Polizzi
1/
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
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
December 4, 2025 at 4:32 PM
1/
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
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
Reposted by Nick Polizzi
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
December 1, 2025 at 2:28 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Nick Polizzi
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
youtu.be/I-utRMS84E8
Learning millisecond protein dynamics from what is missing in NMR spectra
YouTube video by Boston Protein Design and Modeling Club
youtu.be
November 22, 2025 at 1:56 AM
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
youtu.be/I-utRMS84E8
@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...
Google Colab
colab.research.google.com
November 13, 2025 at 7:14 PM
@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...
Reposted by Nick Polizzi
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
"Learning millisecond protein dynamics from what is missing in NMR spectra"
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
November 12, 2025 at 6:18 PM
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
"Learning millisecond protein dynamics from what is missing in NMR spectra"
bpdmc.org
Last week to apply!
We are looking to hire an Assistant/Associate Professor interested in creating an innovative (and exciting) program of research in chemical biology, medicinal chemistry, ML/AI, drug discovery - all in the context of cancer biology!
careers.dana-farber.org/job/11813/as...
careers.dana-farber.org/job/11813/as...
Faculty/Health Educator Job: Assistant/Associate Professor, Chemical Biology at Dana-Farber Cancer Institute in 450 Brookline Ave, Boston, MA
Assistant/Associate Professor, Chemical Biology job
careers.dana-farber.org
October 27, 2025 at 7:01 PM
Last week to apply!
Reposted by Nick Polizzi
thanks everyone who packed the house tonight at @mit.edu for an incredible seminar by @grocklin.bsky.social!
October 23, 2025 at 1:38 AM
thanks everyone who packed the house tonight at @mit.edu for an incredible seminar by @grocklin.bsky.social!
Reposted by Nick Polizzi
quick reminder to come see @grocklin.bsky.social tonight at @mit.edu!
Join us in Room 181, Building 68 @mit.edu on October 22nd 2025 @ 7pm EDT to see @grocklin.bsky.social present a mind blowing amount of data and learn what becomes possible at this scale
"Predicting protein folding stability and aggregation propensity using large-scale experiments"
bpdmc.org
"Predicting protein folding stability and aggregation propensity using large-scale experiments"
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
October 22, 2025 at 2:55 PM
quick reminder to come see @grocklin.bsky.social tonight at @mit.edu!
Reposted by Nick Polizzi
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
For anyone seriously interested in how university endowments work, an excellent wonky reference:
www.nber.org/papers/w32506
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...
www.nber.org
October 21, 2025 at 6:26 PM
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
For anyone seriously interested in how university endowments work, an excellent wonky reference:
www.nber.org/papers/w32506
Reposted by Nick Polizzi
now out in Protein Science! onlinelibrary.wiley.com/doi/10.1002/...
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...
onlinelibrary.wiley.com
October 14, 2025 at 1:35 PM
now out in Protein Science! onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Nick Polizzi
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.
October 8, 2025 at 6:27 PM
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.
Reposted by Nick Polizzi
quick reminder to join us at @danafarber.bsky.social tonight for a spectacular seminar by @marinkazitnik.bsky.social!
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
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
October 1, 2025 at 12:35 PM
quick reminder to join us at @danafarber.bsky.social tonight for a spectacular seminar by @marinkazitnik.bsky.social!
Reposted by Nick Polizzi
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
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
September 26, 2025 at 1:54 PM
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
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
Reposted by Nick Polizzi
Our latest article is now published online! In collaboration with @thompson-lab.bsky.social, Marc Garcia-Borràs, and @ferranfeixas.bsky.social.
Distal Mutations in a Designed Retro-Aldolase Alter Loop Dynamics to Shift and Accelerate the Rate-Limiting Step
pubs.acs.org/doi/full/10....
Distal Mutations in a Designed Retro-Aldolase Alter Loop Dynamics to Shift and Accelerate the Rate-Limiting Step
pubs.acs.org/doi/full/10....
Distal Mutations in a Designed Retro-Aldolase Alter Loop Dynamics to Shift and Accelerate the Rate-Limiting Step
Amino acid residues distant from an enzyme’s active site are known to influence catalysis, but their mechanistic contributions to the catalytic cycle remain poorly understood. Here, we investigate the...
pubs.acs.org
August 26, 2025 at 12:41 PM
Our latest article is now published online! In collaboration with @thompson-lab.bsky.social, Marc Garcia-Borràs, and @ferranfeixas.bsky.social.
Distal Mutations in a Designed Retro-Aldolase Alter Loop Dynamics to Shift and Accelerate the Rate-Limiting Step
pubs.acs.org/doi/full/10....
Distal Mutations in a Designed Retro-Aldolase Alter Loop Dynamics to Shift and Accelerate the Rate-Limiting Step
pubs.acs.org/doi/full/10....
Interested in doing a postdoc at DFCI/Harvard on computationally designing and experimentally characterizing mini-protein binders for biomedical applications? Eric Fischer and I are looking for someone to work in our groups starting asap! Email me or my admin with a CV to apply!
August 19, 2025 at 4:21 PM
Interested in doing a postdoc at DFCI/Harvard on computationally designing and experimentally characterizing mini-protein binders for biomedical applications? Eric Fischer and I are looking for someone to work in our groups starting asap! Email me or my admin with a CV to apply!
Reposted by Nick Polizzi
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
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
August 13, 2025 at 1:52 PM
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
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
Reposted by Nick Polizzi
Happy to see this new T7 replicon based orthogonal replication system in E. coli. Congrats to the Diercks and Schultz lab teams at Scripps Research! www.science.org/doi/10.1126/...
An orthogonal T7 replisome for continuous hypermutation and accelerated evolution in E. coli
Systems that perform continuous hypermutation of designated genes without compromising the integrity of the host genome can substantially accelerate the evolution of new or enhanced protein functions....
www.science.org
August 8, 2025 at 5:37 PM
Happy to see this new T7 replicon based orthogonal replication system in E. coli. Congrats to the Diercks and Schultz lab teams at Scripps Research! www.science.org/doi/10.1126/...
Reposted by Nick Polizzi
Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Scaling down protein language modeling with MSA Pairformer
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...
biorxiv.org
August 5, 2025 at 6:31 AM
Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵