The Tortured Proteins Department

Stephanie Wankowicz
  • 5.0 (4)
  • LIFE SCIENCES
  • UPDATED MONTHLY

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

  1. 1D AGO

    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

  2. FEB 22

    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

    1h 5m

  3. JAN 27

    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

  4. 12/20/2025

    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

    1h 7m

  5. 11/23/2025

    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

    1h 1m

  6. 10/23/2025

    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

    1h 1m

  7. 09/27/2025

    Episode 7: Preprint notifications and the point of rotations

    Latest News: -H1B changes & chaos -Who determines what gets into Pubmed (Literature Selection Technical Review Committee) Preprints: Generative design of novel bacteriophages with genome language models Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles (See great biorxiv comment on the paper!)

    49 min

  8. 08/31/2025

    Episode 6: Open Science and the Future of Engagement

    We chatted about the recent meetings, latest news, open science, social media, and, of course, the recent engagement. Preprints: Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes Computational design of conformation-biasing mutations to alter protein functions Why do we still publish in scientific journals? - Pedro Beltrao's blog The diffUSE Project OpenADMET

    54 min
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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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