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 AlphaFoldProduct-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
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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
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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/10.1101/2025.03.27.644168v1Enthalpy-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=1Conserved energetic changes drive function in an ancient protein fold- https://www.biorxiv.org/content/10.1101/2025.04.02.646877v1
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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
Netherlands