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Joe Greener

@jgreener64.bsky.social
678 followers 516 following 187 posts

Computational chemist/structural bioinformatician working on improving molecular simulation at MRC Laboratory of Molecular Biology. jgreener64.github.io

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Reposted by Joe Greener
Kai Yi @kaiyi94.bsky.social · 29/09/2026
1/7 Excited to share GuideFlip! We use guided discrete flow matching to co-design protein sequences and structures for flexible interactions, with experimental validation across three systems: α-synuclein, RBX1 and active-state GPCR nanobodies.
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Joe Greener @jgreener64.bsky.social · 30/09/2026
I gave a teaching lecture on molecular dynamics this morning. If anyone is interested in the slides they are at docs.google.com/presentation....
docs.google.com
LJC Summer School lecture
Molecular Dynamics Joe Greener MRC Laboratory of Molecular Biology LJC Summer School - 30/09/26
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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026
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...
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Joe Greener @jgreener64.bsky.social · 18/09/2026
Our Garnet paper is now out in final form: a protein and small molecule force field trained from scratch, with competitive results for binding free energy prediction. pubs.rsc.org/sc/article/d...
pubs.rsc.org
Submit This Form
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Sjors Scheres @sjorsscheres.bsky.social · 15/09/2026
Michel Goedert and myself are looking for two postdocs to work on #cryoEM and #masspec of #alphasynuclein filaments from neurodegenerative disease. Come join our bubbly and friendly team at the @mrclmb.ac.uk in lovely Cambridge, UK. www.nature.com/naturecareer...
nature.com
Postdoctoral Scientist | Neurobiology | Dr Michel Goedert | LMB 2842 - Cambridgeshire job with MRC Laboratory of Molecular Biology | 12864505
Postdoctoral Scientist Salary £42,694 per annum Fixed term, 3 years MRC Laboratory of Molecular Biology, Cambridge, UK To work in the group of Dr M...
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Joe Greener @jgreener64.bsky.social · 07/08/2026
Happy to play a small part in this perspective led by @andreasbender.bsky.social on where AI is in drug discovery, and what we should do in future. www.nature.com/articles/s41... Free link: rdcu.be/fyr77
nature.com
Artificial intelligence in drug discovery — what it is, where we stand and the path forward - Nature Reviews Drug Discovery
Applications of artificial intelligence (AI) in drug discovery have attracted high interest in recent years, but evidence for clinically relevant impact so far is limited. This Perspective discusses p...
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Reposted by Joe Greener
Ben Lehner @benlehner.bsky.social · 03/08/2026
1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...
biorxiv.org
Complete Mutagenesis of the Genome and Proteome of ΦX174
The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 01/08/2026
Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek
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Dr Katie Twomey @k2mey.eurosky.social · 29/07/2026
For non-academic people, this how much UK universities pay publishers to publish their researchers’ articles. The publishers don't pay the researchers, and don't pay the peer reviewers. They also frequently cock up your paper at the typesetting stage. Academic publishing is the worst grift.
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Joe Greener @jgreener64.bsky.social · 28/07/2026
Now out as a perspective in PLOS Biology. Where next for structural bioinformatics? journals.plos.org/plosbiology/...
journals.plos.org
Where next for structural bioinformatics?
Structural bioinformatics aims to answer biological questions by considering biomolecular structures at scale. This Perspective argues that now that we have accurate predictions, we need to ask what w...
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Joe Greener @jgreener64.bsky.social · 24/07/2026
I have often seen Microsoft software spread within organisations due to IT and procurement people being "captured" by effective lobbying and sales pitches. Microsoft software is not particularly good, safe or cheap, and researchers benefit from having choice over what they use. @ukri.org
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Joe Greener @jgreener64.bsky.social · 17/07/2026
Function of a protein: something the protein does. Function in maths: a mapping from X to Y. Function in code: re-use code to do a task. Function at a conference: have a drink and look at posters.
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Rob Manuel @robmanuel.b3ta.com · 08/06/2026
Guardian should ask mathematicians to rank the best 100 numbers. This idea occurred to me as a piss take but it could potentially be good.
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Joe Greener @jgreener64.bsky.social · 03/06/2026
Back from parental leave. Thanks to the group for the card, I'm looking forward to the next phase of our science.
Card for congratulations on a new baby with scientific modifications.
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 30/05/2026
Everything you wanted to know about the protein chemistry behind how amino-acid changes affect the cellular abundance of proteins from @tkschulze.bsky.social Effects of residue substitutions on the cellular abundance of proteins doi.org/10.7554/eLif...
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Open Free Energy @openfree.energy · 21/05/2026
This study has been two years in the making and the results have already been widely discussed and compared against, but the paper is finally out in JCIM today! pubs.acs.org/doi/10.1021/...
pubs.acs.org
Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE
Accurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods, hav...
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Simon Hammann @simonhammann.bsky.social · 20/04/2026
Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.
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MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 16/04/2026
The LMB Rising Talent Fellowship is open for new applicants! Aimed at Black heritage scientists, the Fellowship offers a 3-year postdoctoral position beginning Oct-Dec 2026. Visit our website for more info: mrclmb.ac.uk/careers-and-... Please circulate this post to anyone who might be interested!
Announcement for a three-year Rising Talent Fellowship for Black heritage postdoctoral scientists at MRC Laboratory of Molecular Biology.
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 08/04/2026
Exploiting internal symmetry can be a powerful approach to analyse convergence in MD simulations. If two conformational states are symmetry related, their kinetic and thermodynamic properties should be the same. If one doesn't enforce this during analysis this provides a useful test. 1/n
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louiseatkin.bsky.social @louiseatkin.bsky.social · 01/04/2026
Been away from scientific research for over a year and want to get back to the bench? LMB's new Career Returner Fellowship bridges the gap for those who want to re-enter lab-based research. Applications open 13 April More info mrclmb.ac.uk/careers-and-... PLEASE SHARE THIS! @mrclmb.ac.uk
Women scientists look at sample
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Joe Greener @jgreener64.bsky.social · 03/04/2026
"Every hour you spend confused is an hour you spend building the infrastructure inside your own head that will eventually let you do original work."
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Luis Pedro Coelho @luispedrocoelho.bsky.social · 02/04/2026
We have always been overwhelmed by the current data explosion! luispedro.substack.com/p/bioinforma...
luispedro.substack.com
Bioinformaticians have been writing the same abstract for decades
We have always been overwhelmed by the data explosion
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niki grayson @nikigrayson.com · 02/04/2026
i'm so sorry we've sent these souls to the moon and they're using outlook?
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Joe Greener @jgreener64.bsky.social · 01/04/2026
On this 1st April I'm happy to release a technical report from our startup MirageBio, describing a new protein structure model with state-of-the-art performance. jgreener64.github.io/posts/techni...
jgreener64.github.io
MirageBio technical report
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MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 27/03/2026
Join our Scientific Computing team! Work with open source HPC systems, support Linux/Mac/PC environments, script smart solutions & help build in house tech. Great for a curious, creative problem solver. www.nature.com/naturecareer... Apply by 19 APR #ComputingJobs #CambridgeJobs #Hiring
Job opening for Scientific Computing Officer at MRC Laboratory of Molecular Biology focussing on HPC and hands-on open-source computing to support research.
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Kelly Nguyen @kellythd-nguyen.bsky.social · 26/03/2026
Proud to share the yeast telomerase structure, led by the talented @hongmiaohu.bsky.social in collaboration with the Wellinger and Chartrand labs. Discovered 37 years ago and took us nearly 7 years but totally worth the wait 😍. www.science.org/doi/10.1126/... www.youtube.com/watch?v=gFE4...
youtube.com
Cryo-EM structure of yeast telomerase
YouTube video by MRC Laboratory of Molecular Biology
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Joe Greener @jgreener64.bsky.social · 18/03/2026
Check out our pre-print, where we train a protein and small molecule force field from scratch with a graph neural network. We show comparable performance to existing, manually-tuned force fields on a range of tasks including binding free energy prediction. (1/4) arxiv.org/abs/2603.16770
arxiv.org
Training a force field for proteins and small molecules from scratch
Force fields for molecular dynamics are usually developed manually, limiting their transferability and making systematic exploration of functional forms challenging. We developed a graph neural networ...
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Joe Greener @jgreener64.bsky.social · 18/03/2026
arXiv is separating from Cornell University and the Simons Foundation to become an independent non-profit. They are advertising for a CEO whose salary will take ~5% of the budget: jobs.chronicle.com/job/37961678.... I just hope they can maintain the efficient model that has worked well for years.
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Joe Greener @jgreener64.bsky.social · 17/03/2026
Interesting article and visualisations. Hopefully one day we can run all-atom simulations of the nuclear pore.
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 17/03/2026
AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk
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Joe Greener @jgreener64.bsky.social · 06/03/2026
Catch the tiger! www.experimental-history.com/p/the-one-sc...
experimental-history.com
The one science reform we can all agree on, but we're too cowardly to do
OR: the long overdue forest fire
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Joe Greener @jgreener64.bsky.social · 05/03/2026
Fun visit to @bindresearch.org today. They have some great ideas to find drugs that target disordered proteins and to make lots of IDP-ligand data available.
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Reposted by Joe Greener
Robert "The Bobby Yaga" McNees @mcnees.bsky.social · 26/02/2026
There's a "is anyone even reading this" sort of honesty you get in the software update release notes from a project that's been around for a long time.
The screenshot of the release notes reads:

A new version of TeX Live Utility is available!
TeX Live Utility 1.55 is now available-you have 1.54. Would you like to download it now?
Release Notes:
Changes Since 1.54
• Fix bug 137, homepage link in Help Book.
• First release in a long time, since I don't use TeX anymore and resent the very idea of paying Apple annually for the privilege of giving away free and open-source software. Also, I'm really lazy. Please accept my apologies for all the annoying issues you've encountered in this mission-critical software.
• Updated mirror list, which was three years out of date.
• Added missing legacy mirrors, which was even more out of date.
• Added an alert on startup when user tries Homebrew's lobotomized MacTex, because those lunatics left timgr but removed its database.
Thanks for nothing, guys. Bug 142 and 144.
• Use a custom user-agent to work around the Anubis bot trap on texlive.info. Can't wait to see what else breaks because of this, thanks to the profusion of degenerate Artificial Insemination fetishists scraping websites to feed their models.
• Lists of countries in Repository/Continent are now sorted. No idea how you people let me get away with that one for the last fifteen years.
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qntm @qntm.org · 26/02/2026
I can overlook millimetres per year, but what utter anarchy of a unit is inches per megasecond
The Indian plate is part of the Indo-Australian plate, which underlies the Indian Ocean and Bay of Bengal, and is moving north-east at an average of 60 mm/a (0.075 in/Ms).
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MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 25/02/2026
Congratulations to @kellythd-nguyen.bsky.social, Group Leader in the LMB’s Structural Studies Division, who has been named the Life Sciences Laureate at the 2026 Blavatnik Awards in the UK 🎉 Read the full news story here: mrclmb.ac.uk/news-events/... #LMBNews #Blavatnik2026
Kelly Nguyen announced as Laureate in Life Sciences at the 2026 Blavatnik Awards in the UK.
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Joe Greener @jgreener64.bsky.social · 24/02/2026
A great position in our division is now open, do feel free to contact me with questions.
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Joe Greener @jgreener64.bsky.social · 19/02/2026
A useful initiative, as I've noticed that a lot of people use scientific software without citing it.
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Joe Greener @jgreener64.bsky.social · 04/02/2026
I'm seeing a few neural networks that predict very long molecular dynamics time steps, and I'm not convinced that this is the way to go. We often want the trajectory not for its own sake, but in order to get snapshots of the underlying ensemble. (1/4)
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Philip Ball @philipcball.bsky.social · 30/01/2026
I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵 www.nature.com/articles/s41...
nature.com
Advancing regulatory variant effect prediction with AlphaGenome - Nature
AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...
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Cole Group @colegroupncl.bsky.social · 27/01/2026
Now out in JACS! 🎉 : "Computing Solvation Free Energies of Small Molecules with Experimental Accuracy"! It's been a pleasure to collaborate on this with Harry Moore (@jhmchem.bsky.social) & Gábor Csányi pubs.acs.org/doi/10.1021/...
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Milot Mirdita @milot.bsky.social · 20/01/2026
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org
mirdita.org
Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
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Joe Greener @jgreener64.bsky.social · 20/01/2026
Scientific publishing used to be very different, as did science: www.nature.com/articles/248....
nature.com
Building the Tower of Babble - Nature
In remembering, without nostalgia, the dawn of molecular biology, Dr Chargaff deplores the loss of innocence that science has suffered in his lifetime.
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Joe Greener @jgreener64.bsky.social · 14/01/2026
The Big Fantastic Virus Database (BFVD) is now available for searching in Progres v1.1.0. The BFVD is the missing viral bits of the AlphaFold database, and contains a lot of structural diversity. github.com/greener-grou...
github.com
GitHub - greener-group/progres: Fast protein structure searching or your money back
Fast protein structure searching or your money back - greener-group/progres
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Diego del Alamo @delalamo.xyz · 08/01/2026
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Diego del Alamo @delalamo.xyz · 26/12/2025
So 2025 turned out to be a big year for de novo antibody design! Here are thoughts and predictions on the state of de novo antibody design heading into 2026 🧵
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Free Energy Workshop 2025 @feworkshop.bsky.social · 05/01/2026
Exciting news! We have a new website: omsf.io/alchemistry Your one-stop shop for everything related to our conference community. 🎉 BTW, registration is now open, so head over to secure your spot! We'll be sharing updates and details about the event. Bookmark it as there's plenty more to come!
omsf.io
Alchemistry Workshop in Free Energy Methods for Drug Design - Alchemistry
Annual conference on Free Energy Methods in Drug Discovery
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Joe Greener @jgreener64.bsky.social · 19/12/2025
Promising to see open methods for binding free energy prediction improving.
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MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 16/12/2025
Excellent opportunity for a #postdoc to join Michel Goedert’s group, investigating the mechanisms which cause the formation of amyloid filaments in neurodegenerative diseases, in collaboration with @sjorsscheres.bsky.social’s group. More details: www.nature.com/naturecareer... Closes 04 JAN
Michel Goedert, sat in front of a computer screen which displays filament fold structures
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MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 10/12/2025
The LMB is proud to be a founding member of the newly launched National Research Organisations (NRO) Group – a new alliance of 35 UK research centres dedicated to #MakingResearchMatter for people, communities & the economy. Learn more: nrogroup.org #NROGroup #LMBinthenews
National Research Organisations logo, black text on white background surrounded by green and pink lines radiating out from the central text, with Making Research Matter written below
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Sjors Scheres @sjorsscheres.bsky.social · 10/12/2025
Postdoc opportunity with Michel Goedert and myself to work on #cryoEM/#cryoET structures of #amyloids. Feel free to email me with any questions you might have. mrc.tal.net/vx/mobile-0/...
mrc.tal.net
Postdoctoral Scientist - Neurobiology - Dr Michel Goedert - LMB 2752 - Medical Research Council
Location: Cambridge. Vacancy: Postdoctoral Scientist - Neurobiology - Dr Michel Goedert - LMB 2752. Closing Date: 04/01/2026, 23:55
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