Reposted by Joe GreenerKai Yi @kaiyi94.bsky.social · 29/09/20261/7 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. 13425
Joe Greener @jgreener64.bsky.social · 30/09/2026I 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.comLJC Summer School lectureMolecular Dynamics Joe Greener MRC Laboratory of Molecular Biology LJC Summer School - 30/09/26 0194
Reposted by Joe GreenerMartin Pacesa @martinpacesa.bsky.social · 21/09/2026ʙɪɴᴅᴄʀᴀꜰᴛ2 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... 4292142
Joe Greener @jgreener64.bsky.social · 18/09/2026Our 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.orgSubmit This Form 0145
Reposted by Joe GreenerSjors Scheres @sjorsscheres.bsky.social · 15/09/2026Michel 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.comPostdoctoral Scientist | Neurobiology | Dr Michel Goedert | LMB 2842 - Cambridgeshire job with MRC Laboratory of Molecular Biology | 12864505Postdoctoral 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... 01628
Joe Greener @jgreener64.bsky.social · 07/08/2026Happy 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/fyr77nature.comArtificial intelligence in drug discovery — what it is, where we stand and the path forward - Nature Reviews Drug DiscoveryApplications 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... 041
Reposted by Joe GreenerBen Lehner @benlehner.bsky.social · 03/08/20261st 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.orgComplete Mutagenesis of the Genome and Proteome of ΦX174The 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... 19742
Reposted by Joe GreenerMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 01/08/2026Riboseek 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 217975
Reposted by Joe GreenerDr Katie Twomey @k2mey.eurosky.social · 29/07/2026For 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. 35926
Joe Greener @jgreener64.bsky.social · 28/07/2026Now out as a perspective in PLOS Biology. Where next for structural bioinformatics? journals.plos.org/plosbiology/...journals.plos.orgWhere 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... 0258
Joe Greener @jgreener64.bsky.social · 24/07/2026I 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 061
Joe Greener @jgreener64.bsky.social · 17/07/2026Function 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. 092
Reposted by Joe GreenerRob Manuel @robmanuel.b3ta.com · 08/06/2026Guardian should ask mathematicians to rank the best 100 numbers. This idea occurred to me as a piss take but it could potentially be good. 2313119
Joe Greener @jgreener64.bsky.social · 03/06/2026Back from parental leave. Thanks to the group for the card, I'm looking forward to the next phase of our science. 0140
Reposted by Joe GreenerKresten Lindorff-Larsen @lindorfflarsen.bsky.social · 30/05/2026Everything 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... 27021
Reposted by Joe GreenerOpen Free Energy @openfree.energy · 21/05/2026This 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.orgLarge-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFEAccurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods, hav... 082
Reposted by Joe GreenerSimon Hammann @simonhammann.bsky.social · 20/04/2026Don'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. 191957537
Reposted by Joe GreenerMRC Laboratory of Molecular Biology @mrclmb.ac.uk · 16/04/2026The 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! 01212
Reposted by Joe GreenerKresten Lindorff-Larsen @lindorfflarsen.bsky.social · 08/04/2026Exploiting 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 1217
Reposted by Joe Greenerlouiseatkin.bsky.social @louiseatkin.bsky.social · 01/04/2026Been 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 0915
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." 090
Reposted by Joe GreenerLuis Pedro Coelho @luispedrocoelho.bsky.social · 02/04/2026We have always been overwhelmed by the current data explosion! luispedro.substack.com/p/bioinforma...luispedro.substack.comBioinformaticians have been writing the same abstract for decadesWe have always been overwhelmed by the data explosion 1114
Reposted by Joe Greenerniki grayson @nikigrayson.com · 02/04/2026i'm so sorry we've sent these souls to the moon and they're using outlook? 463962480
Joe Greener @jgreener64.bsky.social · 01/04/2026On 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.ioMirageBio technical report 14618
Reposted by Joe GreenerMRC Laboratory of Molecular Biology @mrclmb.ac.uk · 27/03/2026Join 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 023
Reposted by Joe GreenerKelly Nguyen @kellythd-nguyen.bsky.social · 26/03/2026Proud 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.comCryo-EM structure of yeast telomeraseYouTube video by MRC Laboratory of Molecular Biology 920675
Joe Greener @jgreener64.bsky.social · 18/03/2026Check 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/2603.16770arxiv.orgTraining a force field for proteins and small molecules from scratchForce 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... 13613
Joe Greener @jgreener64.bsky.social · 18/03/2026arXiv 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. 040
Joe Greener @jgreener64.bsky.social · 17/03/2026Interesting article and visualisations. Hopefully one day we can run all-atom simulations of the nuclear pore. 032
Reposted by Joe GreenerMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 17/03/2026AlphaFold 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 8263110
Joe Greener @jgreener64.bsky.social · 06/03/2026Catch the tiger! www.experimental-history.com/p/the-one-sc...experimental-history.comThe one science reform we can all agree on, but we're too cowardly to doOR: the long overdue forest fire 000
Joe Greener @jgreener64.bsky.social · 05/03/2026Fun 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. 050
Reposted by Joe GreenerRobert "The Bobby Yaga" McNees @mcnees.bsky.social · 26/02/2026There'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. 181335327
Reposted by Joe Greenerqntm @qntm.org · 26/02/2026I can overlook millimetres per year, but what utter anarchy of a unit is inches per megasecond 2236083
Reposted by Joe GreenerMRC Laboratory of Molecular Biology @mrclmb.ac.uk · 25/02/2026Congratulations 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 27111
Joe Greener @jgreener64.bsky.social · 24/02/2026A great position in our division is now open, do feel free to contact me with questions. 020
Joe Greener @jgreener64.bsky.social · 19/02/2026A useful initiative, as I've noticed that a lot of people use scientific software without citing it. 020
Joe Greener @jgreener64.bsky.social · 04/02/2026I'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) 141
Reposted by Joe GreenerPhilip Ball @philipcball.bsky.social · 30/01/2026I 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.comAdvancing regulatory variant effect prediction with AlphaGenome - NatureAlphaGenome, 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... 218472
Reposted by Joe GreenerCole Group @colegroupncl.bsky.social · 27/01/2026Now 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/... 1298
Reposted by Joe GreenerMilot Mirdita @milot.bsky.social · 20/01/2026My 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.orgmirdita.orgMirdita Lab - Laboratory for Computational Biology & Molecular Machine LearningMirdita Lab builds scalable bioinformatics methods. 710756
Joe Greener @jgreener64.bsky.social · 20/01/2026Scientific publishing used to be very different, as did science: www.nature.com/articles/248....nature.comBuilding the Tower of Babble - NatureIn remembering, without nostalgia, the dawn of molecular biology, Dr Chargaff deplores the loss of innocence that science has suffered in his lifetime. 000
Joe Greener @jgreener64.bsky.social · 14/01/2026The 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.comGitHub - greener-group/progres: Fast protein structure searching or your money backFast protein structure searching or your money back - greener-group/progres 040
Reposted by Joe GreenerDiego del Alamo @delalamo.xyz · 26/12/2025So 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 🧵 14216
Reposted by Joe GreenerFree Energy Workshop 2025 @feworkshop.bsky.social · 05/01/2026Exciting 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.ioAlchemistry Workshop in Free Energy Methods for Drug Design - AlchemistryAnnual conference on Free Energy Methods in Drug Discovery 088
Joe Greener @jgreener64.bsky.social · 19/12/2025Promising to see open methods for binding free energy prediction improving. 050
Reposted by Joe GreenerMRC Laboratory of Molecular Biology @mrclmb.ac.uk · 16/12/2025Excellent 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 0109
Reposted by Joe GreenerMRC Laboratory of Molecular Biology @mrclmb.ac.uk · 10/12/2025The 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 0112
Reposted by Joe GreenerSjors Scheres @sjorsscheres.bsky.social · 10/12/2025Postdoc 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.netPostdoctoral Scientist - Neurobiology - Dr Michel Goedert - LMB 2752 - Medical Research CouncilLocation: Cambridge. Vacancy: Postdoctoral Scientist - Neurobiology - Dr Michel Goedert - LMB 2752. Closing Date: 04/01/2026, 23:55 12123