Joe Grove
@grovearmada.bsky.social
Investigating viruses, using pipettes, #AI and coffee. Learn more at the lab website: https://grovelab.github.io/ Check out our database of viral protein structure predictions: https://viro3d.cvr.gla.ac.uk/ Based at: @cvrinfo.bsky.social
The 2026 volume of the Annual Review of Virology is now online. The most read article is "Studying the Deep Evolution of Viruses in the Era of Artificial Intelligence Structure Prediction" by @spyroslytras.bsky.social @mghafari.bsky.social and @grovearmada.bsky.social 👉 arevie.ws/3TnyXnd
ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...
Aminopeptidase N is a receptor for hedgehog merbecoviruses | @natmicrobiol.nature.com www.nature.com/articles/s41...
Aminopeptidase N is a receptor for hedgehog merbecoviruses - Nature Microbiology
Hedgehog merbecoviruses utilize hedgehog aminopeptidase N, but not the human orthologue, as their entry receptor. Structural resolution of the glycoprotein–receptor interface reveals the molecular int...
nature.com
ColabFold 1.6.3 is out! 2.5x faster, pip-installable, ipSAE+pDockQ2 scores. Thanks Choonghwan Lee, Marielle Russo, Gyuri Kim 🐍pip install colabfold[alphafold] CF2 Sneak Peak with AF3/Boltz/Protenix/ESMFold2… 🐍pip install "colabfold[alphafold3]@git+https://github.com/sokrypton/ColabFold@af3-preview"
I hypothesised scientists can be funny, so I set up an experiment: take 8 academics and apply stand-up comedy, then run! Find out what your index fingers say about you and why Mondays are purple on Mon 28th Sep! £5 tickets using code BRIGHTCLUB: www.thestand.co.uk/performance/... @glasgow.ac.uk
Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)
Re-reading this old article from 2019: Go master quits because AI 'cannot be defeated' www.bbc.com/news/technol... It’s very clear that AI has and will change the playing field (sorry) in many disciplines. If the goal is ‘winning’ this may be an existential crisis for many disciplines.
Go master quits because AI 'cannot be defeated'
Lee Se-dol retires from the game of Go after conceding that computers "cannot be defeated".
bbc.com
I'm really frustrated by the constant fear-mongering about AI-designed superviruses. Can we focus on the things that should actually worry us, such as measles? blog.genesmindsmachines.com/p/im-sorry-y...
I'm sorry, you're not going to die from an AI-engineered supervirus
God save us from economists who think they can competently talk about biology
blog.genesmindsmachines.com
First paper with the lab's affiliation!! ✨✨ summarising some of the cool concepts that the Antigen Evolution & Design Lab will be working on! Together with amazing collaborators @mghafari.bsky.social and @grovearmada.bsky.social www.annualreviews.org/content/jour...
Studying the Deep Evolution of Viruses in the Era of Artificial Intelligence Structure Prediction
High mutation rates erode viral sequence similarity, obscuring deep evolutionary history. While protein structure is far more conserved than sequence, its use in evolutionary studies has historically ...
annualreviews.org
Lab member suggests our new lab motto should be: Take that, evolution! Previous Royle Lab mottos/in-jokes... - Cells don't lie - Papers, Productivity, Hope ✨ - No retreat, no surrender! - We're not impressed until we're “in press”. What's your current lab motto? 🧪
New Experimental Google Colab Notebook now integrates AlphaFold3 with OpenFold3 and py2Dmol: colab.research.google.com/github/sokry... (1/3)
Today my laboratory is thrilled to announce a major breakthrough in the fight against the common cold and other diseases like hand,foot, and mouth disease acute flaccid myelitis caused by picornaviruses. We present the first structure of picornaviral 2C, bound to ssRNA (1/n)
The Thermo Fisher situation keeps getting worse. We've now collected 450+ problematic images presented as verification data in TF's antibody catalog. This includes: 🖌️ Dozens more images with duplications or painting 🖨️ Hundreds of blots that all share the same background (behold slideshow below)
Our two-part analysis of the current MV Hondius Andes virus outbreak is now live, including reconstruction of the outbreak molecular clock dating of the closest known ancestors of the outbreak lineage. Part 1: outbreak sequence reconstruction and rooting virological.org/t/molecular-...
Molecular evolutionary analysis of the current MV Hondius Andes virus outbreak
Preliminary reconstruction of the current MV Hondius Andes virus outbreak sequences Note on data use This is an informal analysis of currently available consensus sequences and is not intended as a fo...
virological.org
With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...
We are incredibly excited to see our most recent story out @nature.com today:HIV triggers CD4-signaling to remodel nuclear pores and license infection!A heroic effort led by our very own @d-mesner.bsky.social & @mattvxwhelan.bsky.social! @blizardinstitute.bsky.social Link: tinyurl.com/HIVNup 1/11
A new family of rolling-circle replication endonucleases widespread in archaeal viruses and plasmids. This family is unrelated to the HUH superfamily Reps, but distantly related to the bacterial Rep_trans enzymes. @narjournal.bsky.social academic.oup.com/nar/article/...
Took a long time to get this done, 2-3 years on Figure 1 alone but glad it's finally out!! www.nature.com/articles/s41...
Heart-nosed bat alphacoronaviruses use human CEACAM6 to enter cells - Nature
Human CEACAM6, which is widely expressed in the lung, is identified as a receptor used by the spike proteins of Cardioderma cor (heart-nosed bat) alphacoronaviruses to enter cells.
nature.com
We did a thing: Scientists find a new way coronaviruses can get into human cells www.cam.ac.uk/research/new...
Scientists find a new way coronaviruses can get into human cells
An international team of researchers has identified an East African bat coronavirus capable of entering human cells.
cam.ac.uk
Great delivery by Sarah Little from @grovearmada.bsky.social team @microbiologysociety.org : Scalable Screening of AI Designed Binders that Prevent Virus Entry
Structures of Marburgvirus glycoprotein and its complex with NPC1 receptor doi.org/10.1038/s415...
Structures of Marburgvirus glycoprotein and its complex with NPC1 receptor - Nature
Marburgvirus glycoprotein binds to the endosomal receptor NPC1 in a distinct orientation with higher affinity compared with Ebola virus glycoprotein, accompanied by fusion-relevant rearrangements...
doi.org
I know I am late to the party on this one, but @thrasherxy.bsky.social's The Viral Underclass is *so* good in analysing why the people most excluded from society are also the people in it who are most likely to experience disease. It's incisive, readable, and defiantly hopeful. And also...
The Trojan Horse is real, and it’s microscopic! 🐴🦠 Our paper is out today in @cellcellpress.bsky.social! We discovered that deltaviruses physically hide INSIDE helper viruses to sneak into new cells. And to prove it, we had to image them from every angle. 🧵👇 www.sciencedirect.com/science/arti...
Deltaviruses spread through a viral Trojan Horse
Hepatitis D-like satellite viruses, known as deltaviruses, have been recently discovered in a wide range of animals. These viruses are thought to expr…
sciencedirect.com
We found a viral Trojan Horse: a virus can hide inside another virus.This one surprised us: deltaviruses don’t just borrow a helper virus. They can travel inside it. A literal Trojan Horse “virus-in-a-virus” route into cells. 🤯 Kudos to 1st author @viroscope.bsky.social and co-authors !
Deltaviruses spread through a viral Trojan Horse
Hepatitis D-like satellite viruses, known as deltaviruses, have been recently discovered in a wide range of animals. These viruses are thought to expr…
sciencedirect.com
“It’s a major advance, on the scale of an AlphaFold4. The problem, of course, is that we know nothing of the details.” Isomorphic Lab’s proprietary drug-discovery model is a major advance go.nature.com/3Mm2ZnQ
‘An AlphaFold 4’ – scientists marvel at DeepMind drug spin-off’s exclusive new AI
Isomorphic Lab’s proprietary drug-discovery model is a major advance, but scientists developing open-source tools are left guessing how to achieve similar results.
go.nature.com
Exploring ICTV virus metadata just got easier on ViralZone — interactive table, instant CSV export, and full search. The new species names are displayed alongside virus names and acronyms. viralzone.expasy.org/resources/VM... (source: ictv.global/vmr)
It is almost five years since I first applied AlphaFold to a handful of viral proteins. Today, hundreds of thousands of predictions and many discoveries later, we are delighted to announce the integration of our Viro3D dataset into the @ebi.embl.org and Google DeepMind AlphaFold Database.
EMBL-EBI@ebi.embl.org · 8mo agoThe AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities. This includes rich datasets for microbes, viruses & parasites associated with tropical diseases. Explore the new datasets in the AlphaFold Database. www.ebi.ac.uk/about/news/u...
Very excited to share our work, a fish herpesvirus' cryo EM structure. It features a long PVAT tail, with new and host-like proteins discovered using modelAngelo, Dali, and Viro3D, including a host-like macrodomain doi.org/10.64898/202... @dbhella.bsky.social @grovearmada.bsky.social
doi.org
