The seventeenth episode of The Tortured Proteins Department is out now!

We discuss travels, awards, federal funding, preprints, and AI workflows for science.

• Apple Podcasts
• Spotify

The sixteenth episode of The Tortured Proteins Department is out now!

We discuss consortium meetings, OMB rules, miniprotein kinase preprints, and differences in scholarly work.

• Apple Podcasts
• Spotify

The fifteenth episode of The Tortured Proteins Department is out now!

We discuss a conformational ensembles conference, NIH policy changes, four preprints, and running.

• Apple Podcasts
• Spotify

The fourteenth episode of The Tortured Proteins Department is out now!

We discuss NIH strategic planning, cryo-EM vitrification effects, agentic workflows, and AI lab guidelines.

• Apple Podcasts
• Spotify

The thirteenth episode of The Tortured Proteins Department is out now!

We discuss NIH funding reports, grant termination demographics, protein design, and AI as graduate students.

• Apple Podcasts
• Spotify

The twelfth episode of The Tortured Proteins Department is out now!

We discuss the Olympics, NIH bureaucracy, preprints on protein regulation and NMR exploration.

• Apple Podcasts
• Spotify

The eleventh episode of The Tortured Proteins Department is out now!

We chat about travels, new preprints, and vibe coding.

Preprints discussed in this episode:

• 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

Links:

• Jeremy Reiter’s gene list

• Spotify
• Apple Podcasts

The tenth episode of The Tortured Proteins Department is out now!

Topics covered:

• Year in review
• 2026 predictions

Links discussed in this episode:

• How to Not Make a Scientific Journal by Accident — Prachee Avasthi’s Substack

Preprints discussed in this episode:

• Rewriting protein alphabets with language models

• Fine-tuning protein language models on human spatial constraint yields state-of-the-art variant effect prediction

• Direct link
• Spotify
• Apple Podcasts

The ninth episode of The Tortured Proteins Department is out now!

Topics covered:

• Government shutdown/reopening
• Travels
• The impact of Jane Richardson
• New science funding structures and Arena BioWorks closing
• AI peer review tools

Links discussed in this episode:

• Big experiments are only big if they can fail

Preprints discussed in this episode:

• Hit or Miss: Understanding Emergence and Absence of Homo-oligomeric Contacts in Protein Language Models

• The Drain of Scientific Publishing

• Direct link
• Spotify
• Apple Podcasts

The eighth episode of The Tortured Proteins Department is out now!

Topics covered:

• Compact for Academic Excellence in Higher Education
• Government shutdown
• HHMI’s new open science policies
• Shrinking PhD pools
• The Nobel Prizes

Preprint discussed in this episode:

• Experiment-guided AlphaFold3 resolves accurate protein ensembles

• Direct link
• Spotify
• Apple Podcasts