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. 13 jun

    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

    55 min.

  2. 8 mei

    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

    54 min.

  3. 6 apr

    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

    56 min.

  4. 22 feb

    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

    1 u 5 m

  5. 27 jan

    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

    52 min.

  6. 20-12-2025

    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

    1 u 7 m

  7. 23-11-2025

    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

    1 u 1 m

  8. 23-10-2025

    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

    1 u 1 m
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Info

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

Informatie

  • Maker
    Stephanie Wankowicz
  • Jaren actief
    2025 - 2026
  • Afleveringen
    15
  • Beoordeling
    Veilig
  • Copyright
    © Stephanie Wankowicz
  • Website van aflevering
    The Tortured Proteins Department

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