The Tortured Proteins Department

Topics:

• Compact for Academic Excellence in Higher Education
• Government Shutdown
• HHMI's new open science policies
• Shrinking PhD pools
• The Nobel Prizes
• The Bear
• TLOS Reactions

Preprint: Experiment-guided AlphaFold3 resolves accurate protein ensembles

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!)

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

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

- 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

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.pdf
AF2χ: Predicting protein side-chain rotamer distributions with AlphaFold2:
https://www.biorxiv.org/content/10.1101/2025.04.16.649219v1.full.pdf

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

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