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

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

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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

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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

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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

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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

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

Latest news: H1B changes and chaos; who determines what gets into PubMed (Literature Selection Technical Review Committee).

Preprints discussed in this episode:

• 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

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

We chatted about recent meetings, latest news, open science, social media, and, of course, the recent engagement.

Preprints and links discussed in this episode:

• 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
• Project diffUSE

• OpenADMET

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

We chatted about the latest news, including the new NIH open access policy, trends observed with scientists using LLMs, and 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)

Preprints discussed in this episode:

• An Evaluation of Biomolecular Energetics Learned by AlphaFold

• Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity

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

We chatted about the latest news, our Conformational Ensembles Conference, vibe coding in science, and the Dipsea and Montpelier Mile races.

Preprints discussed in this episode:

• Multiscale guidance of AlphaFold3 with heterogeneous cryo-EM data

• Boltz-2 Towards Accurate and Efficient Binding Affinity Prediction

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

We discussed grant cancellations, exciting regional meetings and reunions, two fun new preprints, community norms surrounding code release, and the importance of giving kudos.

Preprints discussed in this episode:

• Structures of protein folding intermediates on the ribosome

• AF2χ: Predicting protein side-chain rotamer distributions with AlphaFold2

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