LightNews
nickpolizzi.bsky.social
Nick Polizzi
@nickpolizzi.bsky.social
160 followers 94 following 26 posts
Asst prof at HMS, PI at DFCI Designing proteins polizzilab.org
Posts Media Videos Starter Packs
Reposted by Nick Polizzi
jeffreyjgray.bsky.social
Jeffrey J. Gray @jeffreyjgray.bsky.social · 1d
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.
2 3 5
Reposted by Nick Polizzi
bpdmc.org
Boston Protein Design and Modeling Club @bpdmc.org · 8d
quick reminder to join us at @danafarber.bsky.social tonight for a spectacular seminar by @marinkazitnik.bsky.social!
bpdmc.org
Boston Protein Design and Modeling Club @bpdmc.org · 13d
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
Reposted by Nick Polizzi
bpdmc.org
Boston Protein Design and Modeling Club @bpdmc.org · 13d
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
nickpolizzi.bsky.social
Nick Polizzi @nickpolizzi.bsky.social · 21d
There are several depending on what you want to use it for. LASErMPNN and ligandMPNN can both output rotamers given an input seq. I have more experience with LASEr, which is pretty fast, easy to use for this purpose, and relatively lightweight
2
nickpolizzi.bsky.social
Nick Polizzi @nickpolizzi.bsky.social · Sep 2
Congrats, Daniel! 🥳 Def worth a celebratory Mcflurry🍦
1 2
Reposted by Nick Polizzi
chicalab.bsky.social
Roberto Chica Lab @chicalab.bsky.social · Aug 26
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
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
1 5
nickpolizzi.bsky.social
Nick Polizzi @nickpolizzi.bsky.social · Aug 19
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!
2 3
Reposted by Nick Polizzi
bpdmc.org
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
Reposted by Nick Polizzi
chang-c-liu.bsky.social
Chang Liu @chang-c-liu.bsky.social · Aug 8
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
1 4 15
Reposted by Nick Polizzi
yoakiyama.bsky.social
Yo Akiyama @yoakiyama.bsky.social · Aug 5
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🧵
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
1 43 95
Reposted by Nick Polizzi
sairgoetz.bsky.social
sair like their (they, them) @sairgoetz.bsky.social · Aug 1
The goal is catharsis and cackling.
Boston-area: wanna play w/ soft, magnetic sculptures I made for neuro- & gender-spicy folks? Trans* to the front! No performance experience needed. $300 stipend (+ snacks!) for ~12 hrs collab. #bostonart #transart
Apply by Aug 24: bit.ly/signal-sigil
DM me Qs!
3" reflective cushions (which look white) are laid out on an orange shag carpet spelling the text "wind whip'd words." a dark long-haired cat with white paws about the size of each letter is sprawled out underneath the large words. smaller (digitally overlaid) text is in front of the white paws. that text reads: Open Call for Paid Performance Collaborators, IRL in Boston, trans* folks to the front, apply by Sun, Aug 24, bit.ly/signal-sigil, project made possible by Collective Futures Fund
1 1
nickpolizzi.bsky.social
Nick Polizzi @nickpolizzi.bsky.social · Jul 29
Hats off (or on, rather!) to you and Birte and team!
3
Reposted by Nick Polizzi
workshopmlsb.bsky.social
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · Jul 28
Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!
ginaelnesr.bsky.social
Gina El Nesr @ginaelnesr.bsky.social · Jul 28
The MLSB workshop will be in San Diego, CA (co-located with NeurIPS) this year for its 6th edition in December 🧬🔬

Stay tuned @workshopmlsb.bsky.social as we share details about the stellar lineup of speakers, the official call for papers, and other announcements!🌟
7 15
nickpolizzi.bsky.social
Nick Polizzi @nickpolizzi.bsky.social · Jul 25
Congrats Martin!!
1
Reposted by Nick Polizzi
ardemp.bskyverified.social
Ardem Patapoutian @ardemp.bskyverified.social · Jul 18
I still can’t believe that all NIH grants to my colleagues at Harvard and Harvard Medical School have been nullified. And that, as a nation, we’re somehow okay with this illegal, arbitrary, and petty act. Just think of the consequences: scientists, students, and patients will all suffer.
18 190 560
Reposted by Nick Polizzi
bpdmc.org
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
bpdmc.org
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
Reposted by Nick Polizzi
embo.org
EMBO @embo.org · Jul 7
Learn about #AI tools in #protein #science, including design and engineering, at the EMBO Practical Course "AI for protein design" in Puerto Varas, Chile, 3–9 November 2025.

Deadline: 1 August

meetings.embo.org/event/25-ai-...
#LifeSciences #research #training #ProteinStructure #EMBOevents 🧪
AI for protein design
In the last 5 years, the scientific community has witnessed the development of several AI-based tools for groundbreaking advances in protein science. These tools have enabled scientists to predict pr…
meetings.embo.org
1 8 10
Reposted by Nick Polizzi
jeremymberg.bsky.social
Jeremy Berg @jeremymberg.bsky.social · Jul 3
Now would be really good time to sign on in support of these courageous folks.

We are at 5000 now, let's double that ASAP.

www.standupforscience.net/epa-declarat...
Support EPA Staff Now! — STAND UP FOR SCIENCE
Your solidarity with the EPA heroes increases the pressure on their Administrator Lee Zeldin.
www.standupforscience.net
8 12
Reposted by Nick Polizzi
morganlabatnd.bsky.social
Brittany S. Morgan @morganlabatnd.bsky.social · Jul 3
#MorganLabatND is hiring a research technician!! We are looking for an aspiring biochemistry researcher that shares our community values, is curious about the world around them, and brings a unique perspective to our team. (1/2)

jobs.smartrecruiters.com/UniversityOf...
Research Technician
Company Description: The University of Notre Dame is more than a workplace; it is a vibrant, mission-driven community where every employee is valued and supported. Rooted in a tradition of excellence ...
jobs.smartrecruiters.com
1 3 3
Reposted by Nick Polizzi
bpdmc.org
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
Reposted by Nick Polizzi
milkakostic.bsky.social
Milka Kostic @milkakostic.bsky.social · Jun 30
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...
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
11 11
Reposted by Nick Polizzi
georghochberg.bsky.social
georghochberg.bsky.social @georghochberg.bsky.social · Jun 26
Franziska did a spectacularly successful PhD in my group and to a large extend set up the lab when we first started. I'm extremely happy for her (though not the least bit surprised) that she won these very important awards for her PhD. Watch this one, great things are certain to come.
mpimicrobiomarburg.bsky.social
Max Planck Institute for Terrestrial Microbiology @mpimicrobiomarburg.bsky.social · Jun 26
📢 Congratulations 𝗗𝗿. 𝗙𝗿𝗮𝗻𝘇𝗶𝘀𝗸𝗮 𝗦𝗲𝗻𝗱𝗸𝗲𝗿 for receiving the Otto Hahn Medal and Otto Hahn Award from @maxplanck.de ! 🎉 The honors recognize her exceptional work @georghochberg.bsky.social. 🌟 Exciting times ahead! #MaxPlanck #ResearchExcellence www.mpi-marburg.mpg.de/1511259/2025...
Triple Honours for Franziska Sendker
Dr Franziska Sendker, a former doctoral candidate at the Max Planck Institute for Terrestrial Microbiology, has been awarded the Otto Hahn Medal by the Max Planck Society. The medal honours the outstanding achievements of young scientists and comes with a prize of 7,500 euros. In March 2025, she received the Bayer Pharmaceuticals Doctoral Award from the Society for Biochemistry and Molecular Biology (GBM e.V.), presented at the Mosbach Colloquium. Franziska Sendker's research showed that complex protein forms can arise not only through natural selection, but also through random genetic changes.
www.mpi-marburg.mpg.de
1 5
Reposted by Nick Polizzi
biorxiv-bioinfo.bsky.social
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jun 24
How AlphaFold and related models predict protein-peptide complex structures https://www.biorxiv.org/content/10.1101/2025.06.18.660495v1
2 6
Reposted by Nick Polizzi
mbarniolx.bsky.social
Marta Barniol-Xicota @mbarniolx.bsky.social · Jun 22
📢We are looking for a junior postdoc to join our lab. If you are interested on macrocyclic peptides and cancer immunotherapy, get in touch!

‼️spanish or/and catalan are required, since this position involves teaching duties

📩Deadline extended to June 30th
2 2
Reposted by Nick Polizzi
bpdmc.org
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
3 4