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The Tortured Proteins Department: Daily Summaries Delivered
by Stephanie Wankowicz
A deep dive into scientific discovery and the process of doing science, hosted by Stephanie Wankowicz and James Fraser.
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- 4 days ago54 min
Daylight
We chat about the conformational ensembles conference, NIH-proposed policy changes, 4!! preprints, & running. NIH news:OMB Proposal Blog Post Summary on OMB ProposalRFI to Cap the Number of Simultaneous Research Project Grants Early Independence AwardPreprints:Detection of residual native state entropy changes upon mutation in Fyn SH3Protein-ligand binding kinetics are primarily controlled by the protein, not the ligandESMFold2sampleworks: A Modular Platform for Experimentally Guided Biomolecular Ensemble Generation
- May 8, 202653 min
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 equilibrium populationscryoAgent: An agentic workflow for robust and adaptive end-to-end cryo-EM image processingYou need to make AI guidelines for your labWe’re Training Scientists for a World That No Longer Exists
- Apr 6, 202655 min
Long Live
diffUSE ProjectApril Fools Blog NIH News:Funding CurveDrug Monkey 2025 Grant ReportHow the 2025 NIH grant terminations varied by researchers’ demographic groupsPreprints: Intrinsic dataset features drive mutational effect prediction by protein language modelsRibosome Molecular Aging Shapes Translation DynamicsAI Grad Student:Why I may ‘hire’ AI instead of a graduate studentVibe physics: The AI grad student
- Feb 22, 20261h 5m
Science-ing Through the Lightning Strikes
Topics:OlympicsNIH Bureaucracy - Grants & LeadershipsPreprints12 episodes of TTPD! Claude Code & Slack AppsSan Francisco HalfPreprints: Bidirectional allosteric ligand regulation in a central glycolytic enzyme Large-scale exploration of protein space by automated NMR
- Jan 27, 202652 min
Back to December
Preprints:Improving Cryo-EM Optimization Robustness with an Optimal Transport Loss Function for Noisy ImagesProtein folding success depends on the direction and speed of polypeptide chain appearanceJeremy Reiter's gene list
- Dec 20, 20251h 6m
Science Tree Farm
Year in Review & 2026 PredictionsPreprints:Rewriting protein alphabets with language modelsFine-tuning protein language models on human spatial constraint yields state-of-the-art variant effect predictionPrachee Avasthi Blog Post:How to Not Make a Scientific Journal by Accident
- Nov 23, 20251h 0m
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-oligomeric Contacts in Protein Language ModelsThe Drain of Scientific Publishing Big experiments are only big if they can fail
- Oct 23, 20251h 1m
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 ReactionsPreprint: Experiment-guided AlphaFold3 resolves accurate protein ensembles
About The Tortured Proteins Department
A deep dive into scientific discovery and the process of doing science, hosted by Stephanie Wankowicz and James Fraser.
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