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Sara J. Weaver

@sarajweaver.bsky.social
799 followers 375 following 4 posts

Structural biologist in drug discovery. #CryoEM specialist. #MicroED. X-ray #crystallography. #teamtomo Industry.

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Reposted by Sara J. Weaver
pilarcossio.bsky.social @pilarcossio.bsky.social · 19h
5/5 A dream collaboration 🎉🥳, with theory and experiment hand in hand 🙌 with Deb Maji on the experiments, @steve-bonilla.bsky.social , Alex de Marco @rocovino.bsky.social labs, @larsdingeldein.bsky.social @minhuanli.bsky.social computational front. Check it out: www.biorxiv.org/content/10.6...
biorxiv.org
Quantifying RNA Folding Equilibria from Unclassified Cryo-EM Particle Images
Functional RNA structures are typically far more dynamic than most proteins solved by cryo-electron microscopy (cryo-EM). Flexible junctions and weak tertiary contacts produce broad conformational ens...
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Reposted by Sara J. Weaver
pilarcossio.bsky.social @pilarcossio.bsky.social · 19h
2/5 Our idea: reweight computational RNA ensembles directly against individual, unclassified cryo-EM images, using probabilistic modeling and deep learning. No averaging, so the heterogeneity isn’t thrown away.
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pilarcossio.bsky.social @pilarcossio.bsky.social · 19h
1/5 Cryo-EM gives high-resolution RNA structures, but only when high Mg²⁺ freezes out their motion. At physiological conditions, RNAs are dynamic and 3D reconstruction fails. Can we still learn their folding equilibria? New preprint: yes, straight from the raw particle images👇
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Steve Bonilla @steve-bonilla.bsky.social · 19h
Check the preprint of our exciting collaboration with @pilarcossio.bsky.social and others: Quantifying RNA Folding Equilibria from Unclassfied Cryo-EM Images biorxiv.org/content/10.6... see Pilar's very nice description. Congrats Deb Maji and team!
biorxiv.org
Quantifying RNA Folding Equilibria from Unclassified Cryo-EM Particle Images
Functional RNA structures are typically far more dynamic than most proteins solved by cryo-electron microscopy (cryo-EM). Flexible junctions and weak tertiary contacts produce broad conformational ens...
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Reposted by Sara J. Weaver
Lillie Bell @lilliebell.bsky.social · 12/10/2026
Happy to share my PhD work on the regulatory mechanism of E3 ligase RNF213! RNF213 is not a monomer, but a dimer that switches between inhibited and activated states in an ATP-dependent manner. We tracked the activation mechanism and showed how disease mutations can destabilize the inhibited state.
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Reposted by Sara J. Weaver
cryoEM papers @cryoempapers.bsky.social · 11/10/2026
Ab initio CryoEM maps minimizing preferred orientation problems in heterogeneous mixtures: ReconSIREN www.biorxiv.org/content/10.64898/2026.10.03.756391v1 #cryoEM
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Reposted by Sara J. Weaver
James Fraser @fraserlab.com · 10/10/2026
You might get some useful intel from Karen's recent preprint: www.biorxiv.org/content/10.6...
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Reposted by Sara J. Weaver
James Fraser @fraserlab.com · 10/10/2026
I wanted to highlight the structure prediction track because it features 20 novel CryoEM structures of CYP3A4 bound to ligands, collected by Anna Karen Orta!
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Reposted by Sara J. Weaver
James Fraser @fraserlab.com · 10/10/2026
So if you think you can do structure prediction (or improve structure prediction with MD, etc), you should look at the CYP challenge that we at @openadmet.bsky.social are running right now: huggingface.co/spaces/opena...
huggingface.co
OpenADMET CYP Blind Challenge - a Hugging Face Space by openadmet
This Gradio app lets you join the OpenADMET CYP Inhibition Blind Challenge. Upload a CSV or Parquet file with your regression or classification predictions, or a ZIP archive of PDB structures for t...
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Reposted by Sara J. Weaver
Przemek Dutka @przemekdut.bsky.social · 08/10/2026
Our latest development is now on bioRxiv: cryoSHIELDs — amphipathic peptide additives that make cryo-EM grid prep far more reliable. Tested across 24 protein systems, they enabled the first ABCC6 structure and GPCR–G protein structures at just 0.1–0.5 mg/mL! www.biorxiv.org/content/10.6...
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Reposted by Sara J. Weaver
arXiv cs.LG Machine Learning @cslg-bot.bsky.social · 09/10/2026
Xu Han, Chaozhuo Li, Xiaowei Yuan, Yuancheng Sun, Kang Liu, Qiwei Ye: Learning from Hetero Density for Cryo-EM Protein Reconstruction arxiv.org/abs/2610.11403 arxiv.org/pdf/2610.11403 arxiv.org/html/2610.11403
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Reposted by Sara J. Weaver
cryoEM papers @cryoempapers.bsky.social · 09/10/2026
AI agent supervision of structural model building and refinement www.biorxiv.org/content/10.64898/2026.10.05.756902v1 #cryoEM
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Reposted by Sara J. Weaver
cryoEM papers @cryoempapers.bsky.social · 09/10/2026
CryoCodex: learning discrete structural representations for cryo-EM map post-processing www.biorxiv.org/content/10.64898/2026.09.30.755675v1 #cryoEM
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Reposted by Sara J. Weaver
cryoEM papers @cryoempapers.bsky.social · 09/10/2026
CryoSHIELDs: tunable amphipathic peptide additives for cryo-EM www.biorxiv.org/content/10.64898/2026.10.01.755993v1 #cryoEM
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Reposted by Sara J. Weaver
Marcel Dickmanns | 🌿❄️🔬 @madic.bsky.social · 09/10/2026
If you're looking to really get into the weeds of #cryoET in plant tissue 🌿❄️🔬, our detailed protocol is now out in @bio-protocol.bsky.social 🔗 bio-protocol.org/en/bpdetail?...
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Reposted by Sara J. Weaver
cryoEM papers @cryoempapers.bsky.social · 09/10/2026
Gold Electron Microscopy Grids with Anisotropic Foil Geometry Enable On-Grid Contact Guidance pubmed.ncbi.nlm.nih.gov/42849498/ #cryoEM
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Reposted by Sara J. Weaver
cryoEM papers @cryoempapers.bsky.social · 10/10/2026
Purification-free cryo-EM reveals endogenous assemblies from minute tardigrade samples www.biorxiv.org/content/10.64898/2026.10.08.757488v1 #cryoEM
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Reposted by Sara J. Weaver
Kelvin Lau @klausenhauser on 🙅‍♂️🐘🪡 @klausenhauser.bsky.social · 10/10/2026
Anyone else seen this? CryoEM models without any volume reconstruction. Straight from the micrographs, inferred structures restrained by the actual particle data. So sequence + limited particles = structure?! Bypassing all that time making a map just to still model after arxiv.org/html/2610.01...
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Reposted by Sara J. Weaver
cryoEM papers @cryoempapers.bsky.social · 10/10/2026
Structural thermodynamics by cryo-EM resolves minute energy differences in heterogeneous protein complexes. www.biorxiv.org/content/10.64898/2026.10.07.756995v1 #cryoEM
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Reposted by Sara J. Weaver
Debnath Ghosal @debnathghosal.bsky.social · 07/10/2026
When imaging at high mag using cryo-ET, field of view reduces. How to overcome this limit? How do we get a "bird’s-eye view" without compromising resolution? Our very own @HamishBrown has a solution to this: “montage tomography with a rectangular beam!” www.biorxiv.org/content/10.6...
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Reposted by Sara J. Weaver
bioRxiv Biophysics @biorxiv-biophys.bsky.social · 05/10/2026
Plunge freezing tweezers with ultrasonic excitation for reducing preferred particle orientation in cryo-EM www.biorxiv.org/content/10.64898/20…
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Reposted by Sara J. Weaver
cryoEM papers @cryoempapers.bsky.social · 06/10/2026
PowerFit: An updated framework for fast rigid-body fitting into cryo-EM density maps. www.biorxiv.org/content/10.64898/2026.09.29.755289v1 #cryoEM
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Cathy Spangler @cathyspangler.bsky.social · 22/09/2026
These labels are compatible with STA, and the AuNPs can even help to drive alignment due to the rigid AuNP-Fab conjugation design.
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Cathy Spangler @cathyspangler.bsky.social · 22/09/2026
I'm excited to share our new preprint, where we show that fine-tuning gold nanoparticle conjugation to different Fab structural elements can produce powerful, rigidly coupled, labeling tools for in-situ cryo-ET. Take a look if you want to see an AuNP in an EM map!🔬🧠 www.biorxiv.org/content/10.6...
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Reposted by Sara J. Weaver
bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 01/10/2026
Cryo-tides: synthetic peptides for cryo-EM grid preparation of multi-subunit protein complexes sensitive to the air-water interface www.biorxiv.org/content/10.64898/20…
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Reposted by Sara J. Weaver
Oli Clarke @olibclarke.bsky.social · 30/09/2026
Added a couple of things to coot1-trimmings: * Option to set default model/map appearance to mimic Coot 0.9.x * Metal helper to semi-automatically make links for the current ion * Slider to interactively set map brightness (demos of brightness slider & metal helper in subsequent posts)
github.com
GitHub - olibclarke/coot1-trimmings: Customized keybindings and scripts for Coot 1.x
Customized keybindings and scripts for Coot 1.x. Contribute to olibclarke/coot1-trimmings development by creating an account on GitHub.
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Reposted by Sara J. Weaver
cryoEM papers @cryoempapers.bsky.social · 02/10/2026
Cryo-EM reveals untwisted and non-periodic twist fibrils in ex vivo type B ATTRv-V30M fibrils pubmed.ncbi.nlm.nih.gov/42811947/ #cryoEM
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Reposted by Sara J. Weaver
cryoEM papers @cryoempapers.bsky.social · 02/10/2026
Cryo-tides: synthetic peptides for cryo-EM grid preparation of multi-subunit protein complexes sensitive to the air-water interface www.biorxiv.org/content/10.64898/2026.09.30.755610v1 #cryoEM
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cryoEM papers @cryoempapers.bsky.social · 02/10/2026
ZNFX1, an immunoregulatory RNA helicase and E3 ubiquitin ligase, assembles into pleiomorphic polymers pubmed.ncbi.nlm.nih.gov/42822417/ #cryoEM
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Reposted by Sara J. Weaver
cryoEM papers @cryoempapers.bsky.social · 02/10/2026
CryoConvNeXt enables robust identification of low-abundance molecular species in experimental cryo-EM data pubmed.ncbi.nlm.nih.gov/42818773/ #cryoEM
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Reposted by Sara J. Weaver
Nature Methods @natmethods.nature.com · 02/10/2026
Graphene reservoirs formed over perforated support films precisely control ice thickness during cryo-EM sample preparation. www.nature.com/articles/s41...
nature.com
Control of ice thickness in cryo-EM via confinement - Nature Methods
This study explores the use of graphene reservoirs formed over perforated supporting films as a method to precisely control ice thickness during cryo-EM sample preparation.
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Reposted by Sara J. Weaver
Matt Johnson @drmatthewcjohnson.bsky.social · 11/08/2026
Interested in a career in industry cryoEM? We're hiring! We seek a cryoEM/cryoET expert to join our team at Genentech advance our mission to provide high-resolution structural insights into biological macromolecules involved in health and disease. Apply at: careers.gene.com/us/en/job/20...
careers.gene.com
Systems Specialist II in South San Francisco, California, United States of America | Manufacturing & Engineering at Genentech
Apply for Systems Specialist II job with Genentech in South San Francisco, California, United States of America. Manufacturing & Engineering at Genentech
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Reposted by Sara J. Weaver
Briggs Group @briggsgroup.bsky.social · 21/05/2026
COPII at the ERES in-situ from @dr-downes.bsky.social in the Zanetti lab @giuliazanetti.bsky.social: doi.org/10.1038/s415...
doi.org
In situ cryo-ET defines the ultrastructure of ER exit sites in human cells - Nature Cell Biology
Downes et al. use in situ cryo-electron tomography and super-resolution fluorescence microscopy to define ER exit site architecture in unperturbed human cells. They visualize ribosome-exclusion zones ...
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Reposted by Sara J. Weaver
Briggs Group @briggsgroup.bsky.social · 18/05/2026
The architecture of carriers formed by AP3:ARF1 for lysosomal membrane protein transport: www.science.org/doi/10.1126/.... Work from @jggkaufman.bsky.social, in collaboration with @dgershlick.bsky.social and David Owen. @mpibiochem.bsky.social @thecimr.bsky.social
science.org
Architecture of clathrin-independent AP3:ARF1-coated carriers
AP3 generates clathrin-free carriers on endosomes by organizing via ARF1 dimers into elongated membrane-deforming arrays.
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Reposted by Sara J. Weaver
Delnia Nazari @delnianazari.bsky.social · 28/05/2026
1/I was preparing this slide for my annual doctoral school report presentation, and I thought it was worth sharing here: For a long time, I struggled to align my cryo-ET tilts for the Golgi better, but in the end, it was unsuccessful. For some reason, even though I had good data on tomograms without
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cryoEM papers @cryoempapers.bsky.social · 16/05/2026
Applications and prospects of cryo-electron tomography in drug discovery and understanding disease pubmed.ncbi.nlm.nih.gov/42134002/ #cryoEM
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MiTeGen @mitegen.com · 13/05/2026
Now available - The Nanosoft 8-Pocket Autogrid Box - A #cryoem grid box with 8 pockets designed, shaped & sized for autogrids - Pockets are offset to make autogrid removal easier - Available in 6 colors & with a random, unique 5-digit serial number -> zurl.co/89dEH
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Reposted by Sara J. Weaver
Josy ter Beek @josyterbeek.bsky.social · 29/04/2026
Is there a good #contaminant checklist? Just had to tell a researcher that the sample they have been working on and I ran over the SEC-MALS for them, probably is the infamous ArnA his-tag purification contaminant from E. coli (100% Mw and ext. coeff. match). journals.iucr.org/d/issues/202...
journals.iucr.org
Cryo-EM reveals ArnA contamination during purification of a ciliary protein complex
ArnA contamination was independently observed during the purification of a soluble, low-yield protein complex, leading to an unintended 3.23 Å resolution cryo-EM structure. This work broadens recent f...
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Reposted by Sara J. Weaver
Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · 13/05/2026
Yes, there are several related contaminant lists that are mostly aimed at crystallography. The original is ContaMiner (strube.cbrc.kaust.edu.sa/contaminer/c...) and there are lists underlying SIMBAD in CCP4 and, recently, phasertng.changeling (Phenix, soon CCP4). A list for cryoEM would be great!
strube.cbrc.kaust.edu.sa
ContaMiner
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Dawid Zyla @dzyla.bsky.social · 07/05/2026
Measles is coming back. Until now, we didn't know how human antibodies actually recognize and neutralize the virus. No structure of either measles surface protein bound to a human antibody had ever been reported. We set out to change that.
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Helena Watson @helenawatson.bsky.social · 25/04/2026
Preprint 🧵! I’m really excited to introduce BIGSMALL, an interleaved multi-magnification cryo-ET scheme bridging molecular and cellular scales in a single acquisition! BIGSMALL = 𝐁road 𝐈nformation 𝐆athering 𝐒trategy by 𝐌ultiscale 𝐀cquisition of lame𝐋𝐋a www.biorxiv.org/content/10.6... (1/6)
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Helena Watson @helenawatson.bsky.social · 25/04/2026
BIGSMALL captures both high-resolution structures and large-scale cellular context at the same time, by acquiring high- and low-magnification images at every tilt in a tilt-series. This gives: 🟩 large FOV, low mag tomos 🟥 high res, high mag tomos from the same sample region (2/6)
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Miro Astore @miroastore.bsky.social · 24/04/2026
We just preprinted one of my favorite studies @FlatironInst . I was lucky to be part of an amazing team studying the effects of rapid cooling to preserve samples in cryoEM. Read on to learn about the limits of cryoEM for biophysics and how to overcome them www.biorxiv.org/content/10.6...
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MiTeGen @mitegen.com · 13/04/2026
Now available - The Nanosoft 8-Pocket Autogrid Box - A #cryoem grid box with 8 pockets designed, shaped & sized for autogrids - Pockets are offset to make autogrid removal easier - Available in 6 colors & with a random, unique 5-digit serial number -> zurl.co/89dEH
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Reposted by Sara J. Weaver
Kelvin Lau @klausenhauser on 🙅‍♂️🐘🪡 @klausenhauser.bsky.social · 22/04/2026
Calling all xray structure folks that have worked with denovo proteins. Do you suffer from high rfactors? Myself, someone else I know and now multiple structures all seem to suffer from this. Assuming we all tried our best in model building, what could be some causes?
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Gregor Weiss @weiss-lab.bsky.social · 22/04/2026
New preprint 🚀 ❄️ We developed Autogrid-compatible HPF planchettes that enable direct freezing of clipped EM grids and streamline integration with cryo-FIB workflows ✔️ improved grid stability ✔️ reduced handling ✔️ robust vitrification (🦠 🧫 🧠) A step toward routine HPF for complex samples #teamtomo
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Structura Biotechnology @structurabio.bsky.social · 29/04/2025
Grappling with poorly-resolved ligand binding sites in #cryoEM maps? Check out our new case study on a peptide ligand-bound GPCR showing how practical tips and features in #CryoSPARC v4.7 improve locally refined map quality and reveal clearer ligand density! guide.cryosparc.com/processing-d...
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Sebastian Glatt @sebastianglatt.bsky.social · 30/04/2025
Our work is the first study to provide structures of several tRNAs before and after the introduction of modifications at specific sites. In detail, we analyzed 4 human tRNA species to decipher structural and stability effects induced by the installation of Ψ at single or multiple sites.
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Sebastian Glatt @sebastianglatt.bsky.social · 30/04/2025
We used single particle cryo-EM to directly visualize several human tRNAs and analyze the effects of individual tRNA modifications. To our knowledge, the work presents interpretable maps of the smallest asymmetric particles analyzed by single-particle cryo-EM so far.
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Sebastian Glatt @sebastianglatt.bsky.social · 30/04/2025
We are very excited about our latest work, which just came out @embojournal.org – www.embopress.org/doi/full/10..... The work @MCB_UJ was driven by Anna Biela and Ting-Yu Lin 林亭妤 in collaboration with @jmbujnicki.bsky.social…a short🧵
embopress.org
Determining the effects of pseudouridine incorporation on human tRNAs | The EMBO Journal
imageimagetRNAs harbour a complex set of modifications which are important for their function. Here, single particle cryo-EM, biophysics, and computational analyses of the effects of pseudouridine inc...
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