iiinova — where your digital self keeps evolving

Terra Sztain @terrasztain.bsky.social · 04/11/2025

Preprint update!!! How do mutations impact protein function? The answer is key to understanding evolving pathogens, predicting drug resistance, and designing custom proteins. www.biorxiv.org/content/10.1101/2024.09.20.614179v2

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Terra Sztain @terrasztain.bsky.social · 20/10/2025

Using AI/ML for drug discovery? UM is hiring tenure track faculty at multiple ranks! please share and feel free to reach out if you have any questions. careers.umich.edu/job_detail/2...

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Terra Sztain @terrasztain.bsky.social · 03/10/2025

Grateful I was invited to share our recent efforts searching through sequence, structure, and chemical space to predict and combat antiviral drug resistance at the last Antiviral Drug Discovery (AViDD) Open Science Forum before it went on hold:https://youtu.be/FCZ0lFBs5sQ?si=Y7SBdksMSKI9Yedd

youtu.be

Terra Sztain’s 2025-07-16 Antiviral Drug Discovery (AViDD) Open Science Forum Talk

YouTube video by AViDD Open Science Forum

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Terra Sztain @terrasztain.bsky.social · 08/07/2025

Currently interviewing candidates for Lab Manager Position * expertise conducting high impact research with protein NMR spectroscopy required. * this should be demonstrated by multiple first author publications.

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Terra Sztain @terrasztain.bsky.social · 04/06/2025

Today Mortaza Derakhshani, PhD will be presenting "Enzyme Engineering for Sustainable Nylon Recycling" at the ACS Great Lakes Regional Meeting!

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Terra Sztain @terrasztain.bsky.social · 30/05/2025

PhD student in the lab, Daniel Santos Perez gave his first poster presentation today at the Midwest Theoretical Chemistry Conference! Titled "Weighted ensemble enhanced sampling for the elucidation of drug binding pathways"

1) Free diffusion 2) electrostatic steering 3) encounter complex 4) energy barrier crossing 5) bound complex

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 17/04/2025

AlphaFold is amazing but gives you static structures 🧊 In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃 Code: github.com/KULL-Centre/... Colab: github.com/matteo-cagia...

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Terra Sztain @terrasztain.bsky.social · 12/04/2025

We have Easter eggs on the lab windowsill!!

Robin, round bird with black/ grey top and orange tummy sitting on nest outside window of lab

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Terra Sztain @terrasztain.bsky.social · 09/04/2025

#Compchem experts can do experiments to! Everyone is learning how to test their protein mutation predictions this week 🧪👩‍🔬

Six people in lab coats standing in a circle listening to one explaining protocol

Six people in lab coats (and gloves and eye protection) at the bench with ice buckets and tubes

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John Chodera @jchodera.bsky.social · 25/03/2025

This is the moment we've worked toward for a long time: First public disclosure of the @asapdiscovery.bsky.social pan-coronavirus antiviral aiming to help keep humanity safe from future pandemic threats like MERS-CoV and other bat coronaviruses.

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Terra Sztain @terrasztain.bsky.social · 25/03/2025

Many of the sessions I've been in at #ACSSpring2025 have had almost exclusively (white) male speakers 👀 Can folks please link some of your favorite speakers who could be invited to help balance this?

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Terra Sztain @terrasztain.bsky.social · 24/03/2025

Hard to overhear some of these conversations of those who choose to be silent for fear of being targeted, when many of us dont have a choice of whether or not to be targeted.

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Joachim Frank @joachim123.bsky.social · 24/03/2025

regarding Columbia University, I just learned about this (anonymous) account of negotiations of the Hitler regime in the 1930s with Frankfurt University -- Germany's most prestigious university at the time:

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Keith Trujillo @neurochicano.bsky.social · 22/03/2025

Resources for Federal Scientists from the Union of Concerned Scientists Here are resources to have on hand during the Trump administration. We will continue to update this page as more resources are developed. 🧪 www.ucs.org/resources/re...

ucs.org

Resources for Federal Scientists

Are you a federal scientist, contractor, or federal worker? Here are resources to have on hand during the Trump administration.

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Jesspooka Kant 🎃 @jessdkant.bsky.social · 22/03/2025

Trump just directed the DOJ to attempt to disbar attorneys who take legal action against the executive branch while also indicating they will do the same to immigration attorneys. www.whitehouse.gov/presidential...

For instance, the immigration bar, and powerful Big Law pro bono practices, frequently coach clients to conceal their past or lie about their circumstances when asserting their asylum claims, all in an attempt to circumvent immigration policies enacted to protect our national security and deceive the immigration authorities and courts into granting them undeserved relief. Gathering

To address these concerns,| hereby
direct the Attorney General to seek sanctions
against attorneys and law firms who engage in
frivolous, unreasonable, and vexatious
litigation against the United States or in
matters before executive departments and
agencies of the United States.

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Frank Noe @franknoe.bsky.social · 20/03/2025

It was great to catch up with friends at APS: Pilar Cassio, @rocovino.bsky.social Jutta Rogal, Berend Smit, Tess Smidt and @terrasztain.bsky.social

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Roxane Gay @roxanegay.bsky.social · 19/03/2025

You cannot negotiate with terrorists. If the Ivies give in to any regime demands, the goal posts will move. If the massive ivy endowments aren’t deployed to preserve institutional integrity and academic freedom, what on earth are they for?

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Frank Noe @franknoe.bsky.social · 06/12/2024

Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1...

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Sam Connell @samuelconnell.3i.social · 19/03/2025

This breaks my heart. My salary at St. Jude was paid through our comprehensive cancer center grant. My wife's oncologist is at a comprehensive cancer center. Millions of children and adults with cancer get treatment in these 57 centers around the country. These are essential locations for research.🧪

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Dr. Fiona @fionachembot.bsky.social · 13/03/2025

This was a massive team effort and I'm forever grateful for the full list of authors helping me to drive this one into the endzone! Thank you to Anthony Bogetti, Carla Calvó-Tussell, @mackevinbraza.bsky.social, @lcasalino88.bsky.social, Amanda Gramm, Sean Braet, @miarosenfeld.bsky.social,... (1/2)

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Terra Sztain @terrasztain.bsky.social · 11/03/2025

Excited and honored to be part of such an incredible lineup at the APS meeting next week!!

Physics-Based Machine Learning Workflows and Large Language Models are Here for Physics, (Bio)Chemistry, and Drug Discovery.
3:00 pm – 3:36 pm
Presenter: Teresa Head-Gordon (University of California, Berkeley)
Combining physics and machine learning for computer-aided drug design
3:36 pm – 4:12 pm
Presenter: Terra Sztain (University of Michigan)
Multiscale simulation-guided enzyme nanostructure design for catalysis enhancement
4:12 pm – 4:48 pm
Presenter: Chia-En Chang (University of California, Riverside)
Modeling Molecular Recognition with the Polarizable Gaussian Multipole Model
4:48 pm – 5:24 pm
Presenter: Ray Luo (University of California, Irvine)
Following the Rabbit into Chemical Space
5:24 pm – 6:00 pm
Presenter: Brian Shoichet (University of California, San Francisco)

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John Chodera @jchodera.bsky.social · 19/02/2025

Everything is chaos, but I wanted to share some awesome recent science from the lab that hints at where the future of biomolecular simulation is headed: Foundation simulation models that can be fine-tuned to experimental free energy data to produce systematically more accurate predictions.

Figure 1 from arXiv preprint https://doi.org/10.1101/2025.01.06.631610

Fig. 1 Espaloma is an end-to-end differentiable molecular mechanics parameter assignment scheme for arbitrary organic molecules. Espaloma (extensible surrogate potential optimized by message-passing) is a modular approach for directly computing molecular mechanics force field parameters FFF from a chemical graph G such as a small molecule or biopolymer via a process that is fully differentiable in the model parameters FNN. In Stage 1, a graph neural network is used to generate continuous latent atom embeddings describing local chemical environments from the chemical graph. In Stage 2, these atom embeddings are transformed into feature vectors that preserve appropriate symmetries for atom, bond, angle, and proper/improper torsion inference via Janossy pooling.54 In Stage 3, molecular mechanics parameters are directly predicted from these feature vectors using feed-forward neural networks. This parameter assignment process is performed once per molecular species, allowing the potential energy to be rapidly computed using standard molecular mechanics or molecular dynamics frameworks thereafter. The collection of parameters FNN describing the espaloma model can be considered as the equivalent complete specification of a traditional molecular mechanics force field such as GAFF38,39/AM1-BCC55,56 in that it encodes the equivalent of traditional typing rules, parameter assignment tables, and even partial charge models. Reproduced from ref. 49 with permission from the Royal Society of Chemistry.

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Kimberly Prather PhD @kprather.bsky.social · 18/02/2025

Please wake up USA--we cannot just say "whoops" and hit the rewind button. These actions will lead to decades of irreversible devastation to our planet and future generations if they are not halted immediately. Enough is enough (3/3)

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Giulia Palermo @giuliapalermo.bsky.social · 17/02/2025

🚀 Exciting new poster from our lab at #BPS2025! 🧬 @Ahsan09966804 showcases how #MolecularDynamics & #AI can enhance #CryoEM map refinement. 📍 Catch it at Board 18 (1824-Pos) today, don’t miss out! #Biophysics #CompBio

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Sonya @sonyahanson.bsky.social · 17/02/2025

We are hiring a Flatiron Research Fellow in the Structural Molecular Biophysics team! Experience with cryoEM and/or membrane protein simulations are a plus! Happy to chat in person with anyone at #bps2025 ! apply.interfolio.com/160227

apply.interfolio.com

Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio

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Kevin M. Kruse @kevinmkruse.bsky.social · 09/02/2025

Whenever you hear someone sneer about scientific research that seems useless to them — “they’re studying the spit of lizards?!” — remind them that’s exactly how we got Ozempic. globalnews.ca/news/9793403...

globalnews.ca

How a Canadian scientist and a venomous lizard helped pave the way for Ozempic - National | Globalnews.ca

In 1984, Dr. Daniel Drucker, an endocrinologist from the University of Toronto, discovered a hormone that helped pave the way for popular diabetes drugs such as Ozempic.

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Alejandra Caraballo @esqueer.net · 07/02/2025

All this administration does is put every single nonprofit and institution into a trolley problem of either sacrificing trans people or hurting everyone else by eliminating federal funding. It won't end with us. They'll do this with every minority until it's only white men who are left.

A digitally edited version of the classic "trolley problem" meme is shown. The black-and-white drawing depicts a trolley heading toward a fork in the tracks, with a person standing by a lever to decide which track the trolley will take. On one track, five people are tied up, while on the other track, two people are tied up, with one of them draped in a transgender pride flag. The image is meant to represent a moral dilemma, likely related to discussions on transgender rights and societal choices.

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David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 06/02/2025

🚨Academic scientist friends who are members-ideally leaders- of scientific professional societies, I need your help. 🚨 There is a sign-letter being prepared that will speak out against recent politicization of scientific funding and demonization of scientific researchers. 🧪🌎🦑

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Labfrog @youngfroglab.bsky.social · 06/02/2025

HHMI just cancelled our grant. We were in the second year of developing programs to retain students from all backgrounds in STEM. All that work, all that energy…..I am profoundly disappointed. Well-funded HHMI labs, what do you think of dismantling funding for these training programs?

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Derek Lowe @dereklowe.bsky.social · 05/02/2025

I’ve unfortunately needed to add more material to my post from yesterday. The re-election of Donald Trump is looking like the biggest act of American self-destruction since the Civil War. Same link, new title and some updates.

science.org

Revised and Extended: What's Happening Inside the NIH and NSF

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Kristian G. Andersen @kgandersen.bsky.social · 05/02/2025

Genotype D1.1 of H5N1 confirmed in Nevada cattle, which is the one circulating in birds and not B3.13, causing the wider cattle epizootic in the U.S. In other words, this is a second observed jump from birds into cows. Keep rolling the dice, shall we? www.feedstuffs.com/agribusiness...

feedstuffs.com

New HPAI genotype found in Nevada dairy cows

APHIS confirms first detection of D1.1 genotype in dairy cattle through NMTS testing.

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Rosetta Commons @rosettacommons.bsky.social · 04/02/2025

The RaMP program is still accepting applications till March 1, 2025. This one-year fellowship program is intended for students to gain research experience to succeed in PhD programs. Learn more here: rosettacommons.org/education/ra...

rosettacommons.org

Postbaccalaureate

RaMP: Research and Mentoring for Postbacs: Training Program in Biomolecular Structure Prediction and Design Apply Here! Application Guide The Rosetta Commons Research and Mentoring for Postbaccalur…

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Alex Dickson @dicksonlab.bsky.social · 04/02/2025

Random chemistry question 🧪: what is a small organic molecule that exhibits a well-documented conformational change in two different solvents?

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Alejandra Caraballo @esqueer.net · 04/02/2025

Hey everyone, this is the new LGBTQ litigation bot we put together in partnership with Free Law Project. Follow it to stay up to date on legal developments with LGBTQ related cases and the Trump administration.

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Alejandra Caraballo @esqueer.net · 31/01/2025

This is a 5 alarm fire. They're going to pull down all publicly available data, studies, guidance, etc that involves LGBTQ people so when the worst happens to us, no one will know. They're actively trying to erase us. gizmodo.com/cdc-ordered-...

gizmodo.com

CDC Ordered to Scrub Website of Words Like 'Transgender' and 'LGBT'

A CDC employee spoke with Gizmodo about the

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Mike Dickison @adzebill.bsky.social · 01/02/2025

The Internet Archive has to date downloaded 500 terabytes of US government websites, which it crawls at the end of every presidential term. The whole archive is fully searchable. This effort's housed by a donation-funded nonprofit, not a branch of the US government. blog.archive.org/2024/05/08/e...

blog.archive.org

End of Term Web Archive – Preserving the Transition of a Nation | Internet Archive Blogs

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Terra Sztain @terrasztain.bsky.social · 29/01/2025

‪World affairs have got me down ❤️‍🩹 I can do so little as an individual, but I know I'm not alone. Would love to hear what folks are doing to foster community and safe inclusive spaces within academia right now!! #AcademicChatter #AcademicSky #LGBTQStem #LGBTStem

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Terra Sztain @terrasztain.bsky.social · 21/01/2025

This could be a good time to mention we are looking for a new Lab Manager / Postdoc for the biochemistry lab with expertise protein expression, purification, and protein NMR. Details to follow.

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