The Tortured Proteins Department

Daylight

We chat about the conformational ensembles conference, NIH-proposed policy changes, 4!! preprints, & running. NIH news: OMB Proposal [https://www.federalregister.gov/public-inspection/2026-10817/regulation-for-federal-financial-assistance] Blog Post Summary on OMB Proposal [⁠https://elizabethginexi.substack.com/p/summary-of-key-changes-in-ombs-proposed⁠ ] RFI to Cap the Number of Simultaneous Research Project Grants  [https://grants.nih.gov/grants/guide/notice-files/NOT-OD-26-086.html] Early Independence Award [https://commonfund.nih.gov/earlyindependence] Preprints: Detection of residual native state entropy changes upon mutation in Fyn SH3 [https://arxiv.org/abs/2605.14496] Protein-ligand binding kinetics are primarily controlled by the protein, not the ligand [https://www.biorxiv.org/content/10.64898/2026.05.20.726507v1?rss=1] ESMFold2 [https://biohub.ai/] sampleworks: A Modular Platform for Experimentally Guided Biomolecular Ensemble Generation [https://thestacks.org/publications/sampleworks-release]

Mastermind

NIH Strategic Plan Comments (Due 5/26) [https://grants.nih.gov/news-events/nih-extramural-nexus-news/2026/03/nih-seeks-input-on-framework-for-next-nih-wide-strategic-plan] Preprint: Cooling fast and slow: Characterising the effects of vitrification in cryo-EM and the subsequent recovery of equilibrium populations [https://www.biorxiv.org/content/10.64898/2026.04.21.720011v1] cryoAgent: An agentic workflow for robust and adaptive end-to-end cryo-EM image processing [https://www.biorxiv.org/content/10.64898/2026.04.16.718662v1] You need to make AI guidelines for your lab [https://blekhman.substack.com/p/you-need-to-make-ai-guidelines-for?utm_medium=email] We’re Training Scientists for a World That No Longer Exists [https://sciencepolitics.org/2026/03/18/were-training-scientists-for-a-world-that-no-longer-exists/]

Long Live

diffUSE Project [https://diffuse.science/ ] April Fools Blog [https://jgreener64.github.io/posts/technical_report/] NIH News: Funding Curve [https://grant-witness.us/funding_curves.html] Drug Monkey 2025 Grant Report [⁠https://drugmonkey.wordpress.com/2026/03/06/nih-fy2025-funding-data-finally-emerges-on-report/⁠] How the 2025 NIH grant terminations varied by researchers’ demographic groups [https://www.pnas.org/doi/10.1073/pnas.2527755123] Preprints: Intrinsic dataset features drive mutational effect prediction by protein language models [https://www.biorxiv.org/content/10.64898/2026.03.08.710389v1] Ribosome Molecular Aging Shapes Translation Dynamics [https://www.biorxiv.org/content/10.64898/2026.03.08.710403v1] AI Grad Student: Why I may ‘hire’ AI instead of a graduate student [https://www.science.org/content/article/why-i-may-hire-ai-instead-graduate-student] Vibe physics: The AI grad student [https://www.anthropic.com/research/vibe-physics]

Science-ing Through the Lightning Strikes

Topics: Olympics NIH Bureaucracy - Grants & Leaderships [https://bsky.app/profile/jeremymberg.bsky.social/post/3megymbjnqk2k] Preprints 12 episodes of TTPD! Claude Code & Slack Apps San Francisco Half Preprints: Bidirectional allosteric ligand regulation in a central glycolytic enzyme [https://www.biorxiv.org/content/10.64898/2026.02.05.704047v1] Large-scale exploration of protein space by automated NMR [https://www.biorxiv.org/content/10.64898/2026.02.16.706194v1]

Back to December

Preprints: Improving Cryo-EM Optimization Robustness with an Optimal Transport Loss Function for Noisy Images [https://www.biorxiv.org/content/10.64898/2025.12.23.696001v1] Protein folding success depends on the direction and speed of polypeptide chain appearance [https://www.biorxiv.org/content/10.1101/2025.06.30.662406v1.full] Jeremy Reiter [https://bsky.app/profile/reitergroup.bsky.social/post/3mbclzhebd22z]'s gene list