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Ray Berkeley

@ray-berkeley.bsky.social
126 followers 222 following 5 posts

Postdoc @scripps.edu interested in protein-protein interactions and all things undruggable.

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Reposted by Ray Berkeley
Harmit Singh Malik @harmitmalik.bsky.social · 09/08/2026
I’ve often said (partly tongue in cheek) that spite can be a great motivator. But mudita (freudenfeude), the ability to be truly happy for others’ success, can be a much more reliable way to have a fulfilling career. Even if it can seem that way, science is not a zero sum game. Play the long game.
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Nick Polizzi @nickpolizzi.bsky.social · 26/06/2026
Our lab's paper on the de novo design of small-molecule binding proteins is out! In it, we show how neural nets can be trained and used to design binders to drugs with very high success rates. www.nature.com/articles/s41...
nature.com
Zero-shot design of drug-binding proteins via neural iterative selection−expansion - Nature
 By pairing two neural networks in an iterative optimization algorithm, small-molecule binding proteins can be designed from scratch with high accuracy, affinity and success rates, showing p...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 13/05/2026
If you missed the preprint, now is a good time to read the journal version of @grocklin.bsky.social et al’s fantastic paper on multiplexed HDX measurements Large-scale discovery, analysis and design of protein energy landscapes doi.org/10.1038/s415...
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Ray Berkeley @ray-berkeley.bsky.social · 13/05/2026
Cool figure reporting weekly commits to Google's monorepo (from this 2016 article: dl.acm.org/doi/10.1145/...). It would be cool to see this extended to 2026!
A figure reporting the total number of commits to Google's monorepo split between "human commits" and "total commits"
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Reposted by Ray Berkeley
Brian Cook @bcryo.bsky.social · 23/03/2026
1) The Herzik lab is excited to announce our newest preprint in collaboration with the Grotjahn lab! We have developed a surfactant cocktail that seeks to overcome one of the more nefarious problems in #cryoEM, Air-water interface (AWI)-induced damage and preferred orientation (PO).
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Danielle Grotjahn @nanigrotjahn.bsky.social · 24/03/2026
Fun collaboration with the Herzik lab! Very cool to see #TeamTomo + STA directly capture the effects of the AWI at the single-particle level. we know it’s happening, but it’s striking to see it so clearly!
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Reposted by Ray Berkeley
Carl T. Bergstrom @carlbergstrom.com · 27/01/2026
So initial experiments with Open AI's vibe-coding science tool Prism are going about as well as expected.
Rubbish paper "Is Pee Stored in the Balls" with broken diagram, broken, table, and bullshit text.
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Dan Nomura @dannomura.bsky.social · 14/12/2025
Excited to highlight our latest bioRxiv led by grad student Zoe Duong and Qian Shao. We report a chemistry-centric, chemoproteomics-enabled strategy to discover non-degradative molecular glues for transcriptional rewiring.
🔗 www.biorxiv.org/content/10.6...
biorxiv.org
Discovery of Non-Degradative Covalent Molecular Glues for Transcriptional Reprogramming
Transcriptional reprogramming through induced proximity has emerged as a powerful strategy for modulating the expression of oncogenic and tumor-suppressive genes. Inspired by transcriptional reprogram...
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Reposted by Ray Berkeley
Itay Budin @ibudin.bsky.social · 15/09/2025
Very excited to share new work out today in @natchembio.nature.com on a new approach - FACES - for selectively imaging of phospholipids and other biomolecules at spatial resolutions down to individual membrane leaflets (1/n) www.nature.com/articles/s41...
nature.com
Leaflet-specific phospholipid imaging using genetically encoded proximity sensors - Nature Chemical Biology
An approach combining bioorthogonal chemistry with genetically encoded fluorogen-activating proteins enables subcellular imaging of phospholipids and glycans, as well as the visualization of lipid tra...
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Alex Guseman @alexguseman.bsky.social · 13/08/2025
Thrilled to share this manuscript from my lab where we looked at how glycopolymers that compose the glycocalyx influence protein folding and protein-protein interactions via macromolecular crowding. TLDR: The Glycocalyx stabilizes protein folding and PPIs www.biorxiv.org/content/10.1...
biorxiv.org
Glycopolymers stabilize protein folding and protein-protein interactions via enthalpic interactions
Macromolecular crowding is ubiquitous to physiological environments, perturbing the thermodynamics and kinetics of proteins via excluded volume and nonspecific chemical interactions. While crowding ha...
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Reposted by Ray Berkeley
Chris Parker @chrisgparker.bsky.social · 13/08/2025
Happy to share our contribution to this special issue dedicated to "Proximity-Induced Chemical Biology". We provide our take on targeted protein acetylation. Nice work Wesley and Roy! pubs.acs.org/doi/10.1021/...
pubs.acs.org
Targeted Protein Acetylation Through Chemically Induced Proximity
ConspectusProtein acetylation is a pervasive and reversible post-translational modification (PTM) that impacts various protein features including stability, localization, and interactions and regulate...
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Reposted by Ray Berkeley
fitzpatricklab.bsky.social @fitzpatricklab.bsky.social · 17/06/2025
New preprint from Daniel Du @fitzpatricklab.bsky.social shows #femtosecond light pulses can lens electron beams, promising higher contrast in #cryoET and better aberration correction in #cryoEM tinyurl.com/257sw7j9 Experiments made possible by support from @cziscience.bsky.social #ImagingTheFuture
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Terra Sztain @terrasztain.bsky.social · 21/01/2025
This could be a good time to mention we are looking for a new Lab Manager / Postdoc for the biochemistry lab with expertise protein expression, purification, and protein NMR. Details to follow.
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Chemjobber @chemjobber.bsky.social · 16/01/2025
Mass spec/proteomics chempostdoc in the Ferguson lab, UCSD, La Jolla, CA chemsky 🧪 ⚗️ jobrxiv.org/job/universi...
jobrxiv.org
Research Scientist - Mass spectrometry - Ferguson Lab
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
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Reposted by Ray Berkeley
Nature @nature.com · 13/01/2025
Nature research paper: Structural basis for the conformational protection of nitrogenase from O2 go.nature.com/4aiD344
go.nature.com
Structural basis for the conformational protection of nitrogenase from O2 - Nature
Cryo-electron microscopy of Azotobacter vinelandii FeSII–nitrogenase reveals a core complex of molybdenum–iron proteins (MoFePs), iron proteins (FePs) and FeSII, in which FeSII mediates interactions with MoFeP and FeP to position their FeS clusters in catalytically inactive but O2-protected states.
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Ray Berkeley @ray-berkeley.bsky.social · 09/01/2025
Awesome work from Sarah, @bcryo.bsky.social and friends in the Herzik Lab! It was cool to see this come together in such a short time.
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Ray Berkeley @ray-berkeley.bsky.social · 12/12/2024
Awesome application of biorthogonal chemistry to trap non-ribosomal peptide synthetase complexes for cryo-EM, out yesterday from the Burkart Lab @ucsandiego.bsky.social www.nature.com/articles/s41...
nature.com
Crosslinking intermodular condensation in non-ribosomal peptide biosynthesis - Nature
Structural studies of tyrocidine synthetase using site-selective crosslinking probes to link condensation domains with carrier protein substrates define key interactions and molecular mechanisms of no...
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Ray Berkeley @ray-berkeley.bsky.social · 04/12/2024
What do they keep in here…
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