Ray Berkeley @ray_berkeley
Postdoc @scrippsresearch interested in characterizing protein-protein interactions and all things undruggable. rayberkeley.com La Jolla, San Diego Joined February 2015-
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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…
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
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.
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.
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
Another joyful and unparalleled collaboration with the amazing @DNAmyStrom herself during my postdoc at @brangwynnelab and Kosmrlj groups -- we developed a novel computational framework to study elastocapillary interactions between condensates and fiber networks (in this case…
Another joyful and unparalleled collaboration with the amazing @DNAmyStrom herself during my postdoc at @brangwynnelab and Kosmrlj groups -- we developed a novel computational framework to study elastocapillary interactions between condensates and fiber networks (in this case… https://t.co/wAJqlBgNce
Cool follow-up story from Cravatt lab on covalent targeting of NONO: Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO | bioRxiv biorxiv.org/content/10.110…
Structural diversity and oligomerization of bacterial ubiquitin-like proteins dlvr.it/TLFxcJ
.@SecKennedy - thank you so much for your broad support for gene editing and gene therapies as well as recognizing the importance of Baby KJ’s story and the potential that CRISPR base editing therapies hold for patients with severe genetic diseases. I’m thrilled you have publicly…
.@SecKennedy - thank you so much for your broad support for gene editing and gene therapies as well as recognizing the importance of Baby KJ’s story and the potential that CRISPR base editing therapies hold for patients with severe genetic diseases. I’m thrilled you have publicly…
Complexoform-restricted covalent TRMT112 ligands that allosterically agonize METTL5 biorxiv.org/content/10.110… #biorxiv_biochem
Solving the "replication crisis" is dumb because (1) it's not a crisis, (2) the medicine is worse than the disease. Much of this is because people want science to be more like engineering, and it's not. It's fundamentally different and trying to treat engineering processes like…
ShorterLab @ShorterLab
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