Ray Berkeley
@ray_berkeley
Postdoc @scrippsresearch interested in characterizing protein-protein interactions and all things undruggable.
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Excited to share @Nature: How does naloxone (Narcan) stop an opioid overdose? We determined the first GDP-bound μ-opioid receptor–G protein (wt) structures and found naloxone traps a novel "latent” state, preventing GDP release and G protein activation. 🧵 nature.com/articles/s4158…
Delighted that this work was published today in Nature Chemical Biology! Hoping to continue to advance p53-focused therapeutics towards patient benefit. @nchembio
TP53: - Discovered 45 years ago, most cited gene all time - No therapies - 500 million people currently living will die of TP53 mutant cancers without new therapies Our Preprint: - A general strategy for TP53 missense mutant cancers (majority) with prototype small molecules
🚀 Excited to share our latest @biorxivpreprint by @CEStieger We unveil TRACERs - Transcriptional Regulation via Active Control of Epigenetic Reprogramming - a new small-molecule-based induced-proximity modality that silences transcription factors by recruiting endogenous…
Check out our recent collaboration with @abbvie in @CellChemBiol. We identifed compounds that potently clear tau aggregates. After chemoproteomics and functional studies, we found it covalently targets ER protein P4HB (after metabolic activation). sciencedirect.com/science/articl…
Five years ago, in October 2020, my institute appointed me to a full professorship. On this occasion, I select 10 representative research papers we published in the past 5 years. It's been an absolute privilege to work with my super-talented, industrious, and fearless students.
Happy to share that after a long-drawn-out process, my institute has removed the first word of my academic rank. First time in my academic life, I have got a "one-word" description of my position. I thank my incredible students for their contributions and my family for support.😀
Disagree vehemently. It misses the unique needs of medicine and STEM fields where high-value contributions aren’t always tied to high compensation. It risks creating barriers for essential talent in those areas.
If you think LLMs are going to solve drug discovery on their own, and wanna sober up this is a pretty good talk to start with. youtube.com/watch?v=OjvftH…
youtube.com
YouTube
Understanding How Drugs Interact With Anti-Targets: The "Avoid-ome"
In addition to just thinking the work is cool, I'm really proud of the symbiotic relationship teamtomo.org has developed with the Lucas lab over the past year while they built their extensible implementation of 2DTM #OpenSoftwareAcceleratesScience
1/13 🧵 Today, Bindcraft was published in @Nature , one of the most famous AIs in biology for designing protein–protein interactions (PPI). In my opinion. Bindcraft represents one of the most important advances in the post–AlphaFold2 era.
Excited to share my talk hosted by UCTV "A Closer Look at…Genetic Medicine and Artificial Intelligence" discussing RNA, AI and genetic medicine. Together with @KomorLab youtu.be/SSpE8BNOebg?si… via @YouTube
youtube.com
YouTube
A Closer Look at…Genetic Medicine and Artificial Intelligence
We mapped the zinc‑finger (ZF) “degrome.” High‑throughput ZF reporters + glutarimide analogs → new CRBN‑recruited degrons and design rules for degraders.
What’s the next PDB? Maybe it’s …the PDB. We just launched @diffUSEproject, a structural biology initiative exploring protein motion & rethinking how we generate and use experimental data. Quick 🧵👇 diffuse.science
We are thrilled to be part of Project Diffuse, building infrastructure for the dynamic future of structural biology. We are co-leading the modeling and encoding efforts of this project, including developing infrastructure to enable AI to learn from experimental data directly.
Announcing the Diffuse Project! We're unlocking protein dynamics through diffuse X-ray scattering - the overlooked signal that could revolutionize how we understand protein motion. seemay.substack.com/p/from-systems…
Depletion of a transcriptional factor ZBTB11 using molecular glue degraders can overcome oxidative-phosphorylation-mediated KRAS inhibitor resistance in pancreatic ductal adenocarcinoma with low acute neurotoxicity nature.com/articles/s4158…
The OpenADMET teams are cranking away. @jchodera @fraser_lab and I started to formalize the organization and we will have a lot more exciting news in the coming months. For now, here is the hello world blog post: openadmet.org/community/blog…
New work introducing PCIPs, heterobifunctional chemical inducers of proximity that inhibit DNA repair by recruiting BET proteins to PARP2. Great work uncovering a new form of event-driven pharmacology by Bryce/Eric/Erin and the rest of the team. (1/3) biorxiv.org/content/10.110…
What if protein function could be triggered only when the right cell cues are present? With SMART, we combine split inteins and logic gating to create a programmable system for cell-specific protein ligation, thus opening new doors for synthetic biology and cell targeting.
After many months heads down, we at Decade are growing! We are hiring a protein biochemist to help us radically improve cancer treatment. If you like being early and making an impact, we are interested to hear from you! Details here: decade.bio/careers
Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb) was rejected this year. Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology” More on the future of MLSB soon…
My lab’s 5-year NIH R01 grant, awarded to study gene therapy for hearing loss, was abruptly terminated. I want to share how this action has been incredibly harmful and disruptive, not just to my lab, but to the scientific process itself. 1/15
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