The Tortured Proteins Department

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 scholarly work.

Preprints/Blogs:
De novo design of selective kinase modulators
Selective miniprotein inhibitors of Aurora-A kinase designed using interaction-motif scaffolding

Ensemble refinement produces consistent R-free values but smaller ensemble sizes than previously reported

News Links:
Bethesda Declaration one year later
The Public Rejects OMB's Federal Financial Assistance Rule

We chat about the conformational ensembles conference, NIH-proposed policy changes, 4!! preprints, & running.

NIH news:
OMB Proposal
Blog Post Summary on OMB Proposal
RFI to Cap the Number of Simultaneous Research Project Grants 
Early Independence Award

Preprints:
Detection of residual native state entropy changes upon mutation in Fyn SH3
Protein-ligand binding kinetics are primarily controlled by the protein, not the ligand
ESMFold2
sampleworks: A Modular Platform for Experimentally Guided Biomolecular Ensemble Generation

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 equilibrium populations
cryoAgent: An agentic workflow for robust and adaptive end-to-end cryo-EM image processing

You need to make AI guidelines for your lab
We’re Training Scientists for a World That No Longer Exists

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

Preprints:
Intrinsic dataset features drive mutational effect prediction by protein language models
Ribosome Molecular Aging Shapes Translation Dynamics

AI Grad Student:
Why I may ‘hire’ AI instead of a graduate student
Vibe physics: The AI grad student

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

Preprints:
Bidirectional allosteric ligand regulation in a central glycolytic enzyme
Large-scale exploration of protein space by automated NMR