The Tortured Proteins Department

Prism: Unlocking Protein Dynamics

Learn more: prismscience.org

State of Decay

We talk about a big travel month (including Stephanie winning the George Sheldrick Award for Structural Science), federal funding in light of the upcoming turnover of US

Cruel Kinase Summer

We chat about a revolving door of consortium meetings for Jaime, follow up on the OMB proposed rule, two mini-protein kinase preprints, and differences between blogs and

Daylight

We chat about the conformational ensembles conference, NIH-proposed policy changes, 4!! preprints, & running. NIH news: OMB Proposal Blog Post Summary on OMB Proposa

Mastermind

NIH Strategic Plan Comments (Due 5/26) Preprint: Cooling fast and slow: Characterising the effects of vitrification in cryo-EM and the subsequent recovery of equilibri

Long Live

diffUSE Project April Fools Blog NIH News: Funding Curve Drug Monkey 2025 Grant Report How the 2025 NIH grant terminations varied by researchers’ demographic groups

Science-ing Through the Lightning Strikes

Topics: Olympics NIH Bureaucracy - Grants & Leaderships Preprints 12 episodes of TTPD! Claude Code & Slack Apps San Francisco Half Preprints: Bidirectional allo

Back to December

Preprints: Improving Cryo-EM Optimization Robustness with an Optimal Transport Loss Function for Noisy Images Protein folding success depends on the direction and speed

Science Tree Farm

Year in Review & 2026 Predictions Preprints: Rewriting protein alphabets with language models Fine-tuning protein language models on human spatial constraint yields st

Episode 9: I Can Do It With a Broken Grant Cycle

Topics: Government Shutdown/ReopeningTravels The impact of Jane RichardsonAI Peer Review toolsPreprint 1: Hit or Miss: Understanding Emergence and Absence of Homo-oligom

Episode 8: Open Science in a Changing Academic World

Topics: Compact for Academic Excellence in Higher EducationGovernment ShutdownHHMI's new open science policiesShrinking PhD poolsThe Nobel PrizesThe BearTLOS Reactions

Episode 7: Preprint notifications and the point of rotations

Latest News: -H1B changes & chaos -Who determines what gets into Pubmed (Literature Selection Technical Review Committee) Preprints: Generative design of novel bacte

Episode 6: Open Science and the Future of Engagement

We chatted about the recent meetings, latest news, open science, social media, and, of course, the recent engagement. Preprints: Aromatic Ring Flips Reveal Reshaping of

Episode 5: NIH Ghosting, Open Access Policies, and Scientists' interaction with LLMs

We chatted about the latest news, including the new NIH open access policy, trends observed with scientists using LLMs, & the Montpelier Mile race. "The new Administrat

Episode 4: Conformational Ensembles & Teaching Vibe Coding

- News round-up - Conformational Ensembles Conference - Preprints discussed: Multiscale guidance of AlphaFold3 with heterogeneous cryo-EM data (https://www.arxiv.org/

Episode 3: Travels, Protein Folding, Side Chain Dynamics, and Strava Kudos

The preprints discussed in this episode. Structures of protein folding intermediates on the ribosome: https://www.biorxiv.org/content/10.1101/2025.04.07.647236v1.full.p

Episode 2: Cool Science Among Continued Uncertainty

We chatted about the continued chaos of science infrastructure and dived into some cool science from recent meetings Jaime and Stephanie attended. We introduce two new se

Scientific Uncertainty and Graduate Education

Episode 1. We discuss the declining support of science in the US and how it may impact the future of graduate science education. Recorded- 3/14/2025