Stephanie Wankowicz

The Diffuse Project is looking for an amazing Project Manager to help us achieve our goal of unlocking protein dynamics! Are you a scientist who naturally loves organization, coordination, problem solving and working with a diverse team of scientists & engineers?

TTPD #7 with @fraserlab.com.

We chatted about the recent meetings, news, preprint engagement notifications, and the point of rotations.
wankowiczlab.com/2025/09/27/T...
Spotify: open.spotify.com/episode/0JCB...

Runner wedding bliss!

High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles Despite recent advances in data acquisition and algorithmic development, applying single particle cryogenic electron microscopy (cryoEM) to small proteins (<50kDa) remains challenging, even when high ...

Preprint #3: High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles www.biorxiv.org/content/10.1... @olibclarke.bsky.social

Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching Visualizing the structures of small proteins and complexes has been a longstanding challenge in single-particle cryo-EM. Some of these targets have been successfully resolved by binding to antibody fr...

Preprint #2: Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching www.biorxiv.org/content/10.1... @grigoriefflab.bsky.social @kekexinz.bsky.social

Preprint #1: Generative design of novel bacteriophages with genome language models
www.biorxiv.org/content/10.1... @brianhie.bsky.social @samuelhking.bsky.social @claudiadriscoll.bsky.social

TTPD #7 with @fraserlab.com.

We chatted about the recent meetings, news, preprint engagement notifications, and the point of rotations.
wankowiczlab.com/2025/09/27/T...
Spotify: open.spotify.com/episode/0JCB...

This is scary

With a new collaboration called diffUSE, the @stephanieaw.bsky.social lab is helping to advance our understanding of protein motion, leading to a new paradigm in dynamic structural biology.
@vubasicsciences.bsky.social
medschool.vanderbilt.edu/basic-scienc...

What if NIH had been 40% smaller? Replaying history with less NIH funding shows widespread impacts on drug-linked research

This may be the most important paper ever published about NIH funded research.

www.science.org/doi/10.1126/...

Fall beamtime begins! Here is Sarah @andolab.bsky.social ! 😎⚡️

@diffuseproject.bsky.social

A joy we can all agree we need in our lives right now.

🚀 Check out our new preprint on extending the scope of single-particle cryo-EM with 2D template matching!
Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching is now available on bioRxiv!
www.biorxiv.org/content/10.1...

Peak millennial humor.

As always, feedback is always appreciated!

Rules include: define biological selection criteria, set up QC, beware PDB biases, mind sample size/stats/uncertainty, choose proper controls, compare metrics consistently, link to other databases, and visualize everything!

I originally put this guide together for my lab, but expanded it into a “10 Rules” article on how to use structural bioinformatics effectively.

10 Rules for a Structural Bioinformatic Analysis The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins thes...

Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...

Why do people think they will get away with lying on their resume?

These statements about corruption in science are egregious lies. Kennedy is a tsunami of anti-science propaganda.

This isn’t just a moral injury to scientists, it is downright dangerous.

It is devastating that the U.S. Senate is permitting this.

@aliceyting.bsky.social

@paulschanda.bsky.social

Thank you! I hope we don't disappoint too badly with other episodes (but we have improved with every recording!).

The Tortured Proteins Department Life Sciences Podcast · Updated Monthly · A deep dive into scientific discovery and the process of doing science, hosted by Stephanie Wankowicz and James Fraser.

Today, I'm grateful for the podcast The Tortured Proteins Department. Excellent back-and-forth between @fraserlab.com and @stephanieaw.bsky.social. Disclaimer: I've only listened to episode 6; I hope it's not an outlier! 🤪

podcasts.apple.com/us/podcast/t...

Yes, we also reviewed this paper! Excited to read your review.

Open science projects:

Project diffUSE: diffuse.science
OpenADMET: openadmet.org

@diffuseproject.bsky.social @openadmet.bsky.social @seemaychou.bsky.social @pracheeac.bsky.social @jchodera.bsky.social

Why do we still publish in scientific journals ? We publish in scientific journals to disclose our discoveries, such that others can build upon them. But we now have preprint servers and we...

@pedrobeltrao.bsky.social blog: www.evocellnet.com/2025/07/why-...

Computational design of conformation-biasing mutations to alter protein functions Most natural proteins alternate between distinct conformational states, each associated with specific functions. Intentional manipulation of conformational equilibria could lead to improved or altered...

Preprint #2: Computational design of conformation-biasing mutations to alter protein functions www.biorxiv.org/content/10.1...

Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts al...

Preprint #1: Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes
www.biorxiv.org/content/10.1...

Episode 6: Open Science and the Future of Engagement Podcast Episode · The Tortured Proteins Department · 08/31/2025 · 54m

TTPD #6 with @fraserlab.com. We chatted about the recent meetings, latest news, open science, social media, and, of course, the recent engagement.

podcasts.apple.com/us/podcast/e...

wankowiczlab.com/2025/08/31/T...