The Tortured Proteins Department

Stephanie Wankowicz
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A deep dive into scientific discovery and the process of doing science, hosted by Stephanie Wankowicz and James Fraser.

  1. ١٣ يونيو

    Daylight

    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

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  2. ٨ مايو

    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 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

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  3. ٦ أبريل

    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 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

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  4. ٢٢ فبراير

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

    ١ س ٥ د

  5. ٢٧ يناير

    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 of polypeptide chain appearance Jeremy Reiter's gene list

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  6. ٢٠‏/١٢‏/٢٠٢٥

    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 state-of-the-art variant effect prediction Prachee Avasthi Blog Post: How to Not Make a Scientific Journal by Accident

    ١ س ٧ د

  7. ٢٣‏/١١‏/٢٠٢٥

    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

    ١ س ١ د

  8. ٢٣‏/١٠‏/٢٠٢٥

    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 Preprint: Experiment-guided AlphaFold3 resolves accurate protein ensembles

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A deep dive into scientific discovery and the process of doing science, hosted by Stephanie Wankowicz and James Fraser.

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  • صناع العمل
    Stephanie Wankowicz
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  • التقييم
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  • حقوق النشر
    © Stephanie Wankowicz
  • موقع البرنامج على الويب
    The Tortured Proteins Department

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