The Tortured Proteins Department

Stephanie Wankowicz
  • 5.0 (3)
  • LIFE SCIENCES
  • UPDATED MONTHLY

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

Episodes

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 07/13/2025

    Episode 5: NIH Ghosting, Open Access Policies, and Scientists' interaction with LLMs

    We chatted about the latest news, including the new NIH open access policy, trends observed with scientists using LLMs, & the Montpelier Mile race. "The new Administration began weaponizing what should not be weaponized - the health of all Americans...creating chaos and promoting an...unreasoned agenda of blacklisting certain topics, that...has absolutely nothing to do with the promotion of science." - Judge William Young (reported by Max Kozlov, Nature News) An Evaluation of Biomolecular Energetics Learned by AlphaFold Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity

    53 min

  8. 06/14/2025

    Episode 4: Conformational Ensembles & Teaching Vibe Coding

    - News round-up - Conformational Ensembles Conference - Preprints discussed: Multiscale guidance of AlphaFold3 with heterogeneous cryo-EM data (https://www.arxiv.org/abs/2506.04490) Boltz-2 Towards Accurate and EfficientBinding Affinity Prediction (https://jeremywohlwend.com/assets/boltz2.pdf) - Guiding vibe coding for science -Dipsea & Montpelier Mile

    40 min

  9. 05/16/2025

    Episode 3: Travels, Protein Folding, Side Chain Dynamics, and Strava Kudos

    The preprints discussed in this episode. Structures of protein folding intermediates on the ribosome:https://www.biorxiv.org/content/10.1101/2025.04.07.647236v1.full.pdfAF2χ: Predicting protein side-chain rotamer distributions with AlphaFold2:https://www.biorxiv.org/content/10.1101/2025.04.16.649219v1.full.pdf

    58 min

  10. 04/15/2025

    Episode 2: Cool Science Among Continued Uncertainty

    We chatted about the continued chaos of science infrastructure and dived into some cool science from recent meetings Jaime and Stephanie attended. We introduce two new segments: preprints and how to do science. The pre-prints discussed in this episode: Counting particles could give wrong probabilities in Cryo-Electron Microscopy- https://www.biorxiv.org/content/10.1101/2025.03.27.644168v1 Enthalpy-entropy trade-offs in the evolution of ligand specificity in a superfamily of transcription factors- https://www.biorxiv.org/content/10.1101/2025.03.23.644840v1?rss=1 Conserved energetic changes drive function in an ancient protein fold- https://www.biorxiv.org/content/10.1101/2025.04.02.646877v1

    47 min

  11. 03/16/2025

    Scientific Uncertainty and Graduate Education

    Episode 1. We discuss the declining support of science in the US and how it may impact the future of graduate science education. Recorded- 3/14/2025

    44 min
  • 11 Episodes

Ratings & Reviews

5
out of 5
3 Ratings

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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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