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John P. Overington

@jpoverington.bsky.social
980 followers 1.4K following 118 posts

Work at xymeai - Data Science, Cheminformatics, Computational Medicinal Chemistry, Structural Bioinformatics, Protein Engineering, SaaS, DaaS, AI/ML scholar.google.com/citations?user=5…

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John P. Overington @jpoverington.bsky.social · 15/03/2026
Finally mounted my patternmakers nice on the bench. Five axes!
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John P. Overington @jpoverington.bsky.social · 08/03/2026
Lovely day out in the Gulf.
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John P. Overington @jpoverington.bsky.social · 02/03/2026
Was browsing an antique book store in Houston this afternoon and found the treasure. 1959, at the cusp of the molecular biology revolution.
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John P. Overington @jpoverington.bsky.social · 09/02/2026
Does anyone know of a whitespace markup plugin for safari. You know, turns that pesky hidden text to red/green whatever?
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John P. Overington @jpoverington.bsky.social · 01/02/2026
Looks like the cold weather in Houston is over for now, so my best buddies are out of their cover and getting a tan again. The bigger ones should move out of the house later. But one of them flowered like crazy when moved inside.
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John P. Overington @jpoverington.bsky.social · 29/01/2026
I’m looking for a consultant for some part time remote work. Ideal profile would be 25+ years in med chem/pharmacology, remembers the mergers and acquisitions that happened in pharma and is a dab hand at navigating research codes like CS-045, CI-911 and GR-92132X. If this sounds fun, get in touch!
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John P. Overington @jpoverington.bsky.social · 02/01/2026
Spent the early part of the afternoon curating some of the Lego and framing the new portrait.
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John P. Overington @jpoverington.bsky.social · 02/01/2026
The BBC news site is usually great, but I wish that health stories were better proof read and verified. For example, this article mentions the gas nitric acid www.bbc.com/future/artic... of course, it should be nitric oxide.
bbc.com
The surprising benefits of a glass of orange juice
The habit of drinking a glass of orange juice can have a considerable effect on your health.
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John P. Overington @jpoverington.bsky.social · 22/12/2025
Went to Barnes and Noble today to buy some Xmas presents for the family. Ended up getting me a present instead. It is a superb book so far.
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John P. Overington @jpoverington.bsky.social · 30/11/2025
Today I have mostly been sorting the garage.
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John P. Overington @jpoverington.bsky.social · 30/09/2025
Apparently it’s 48 years ago since New Boots and Panties was released. A true classic album, survived the test of time for sure!
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John P. Overington @jpoverington.bsky.social · 26/09/2025
For self conscious pseudo-intellectual teenagers from post-industrial Britain in the 1980s this is big news. For the rest of the world - nothing to see here.
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Reposted by John P. Overington
Andrew White 🐦‍⬛ @andrew.diffuse.one · 26/09/2025
I finished my estimate on required compute to make an atomic-resolution virtual cell: 10^38 FLOPs to simulate a human cell for 1 day. We should be able to do this simulation in 2074 using 200 TW of power. 1/3
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John P. Overington @jpoverington.bsky.social · 24/09/2025
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John P. Overington @jpoverington.bsky.social · 07/09/2025
Nostalgia ain’t what it used to be. Just found a microfiche. Big stack of these. If only I had the reader. I bet they’re museum pieces now.
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John P. Overington @jpoverington.bsky.social · 07/09/2025
Just sorting through some old files. Really fun to step back in time. This must have been 1988 or so. Acetates, permanent markers. None of your AI assistants in putting this together. And it shows 😂😂
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John P. Overington @jpoverington.bsky.social · 01/09/2025
As a Brit expat in the States, it’s sad to see that access to the BBC News website is now paywalled. $90 a year!
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John P. Overington @jpoverington.bsky.social · 22/08/2025
It’s August in our home, and that means getting ready for Halloween!! The theme this year (apparently) is Labyrinth - here is David Bowie.
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John P. Overington @jpoverington.bsky.social · 14/08/2025
A sort of nerdy question around licenses. Imagine I subscribe to a journal in which they don’t allow text mining on the content. Seems fair. But if is store the pdf locally, then my Mac will index it and allow full text searching. Does this count as text mining?
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John P. Overington @jpoverington.bsky.social · 05/08/2025
Getting frustrated with the number of resources that disappear, change terms of use, etc. Seems cheeky that people publish in places like NAR Database with an 'open' resource, then flip to closed. Tempted to put together a table of all the NAR DB resources and plot existence/current license....
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John P. Overington @jpoverington.bsky.social · 20/07/2025
And while I’m thinking of Nature, their typography has gone downhill. The spacing between words in titles is now atrocious! Defense against OCR LLM tokenization or just poor visual design? 🤣
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John P. Overington @jpoverington.bsky.social · 20/07/2025
Bit of an insult for Nature magazine in the Google response to asking if fake patents and fake publications are different.
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Reposted by John P. Overington
Stephen Curry @scurry.bsky.social · 16/07/2025
The times they are a changin’.
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Reposted by John P. Overington
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 02/07/2025
CASP is the main reason the protein structure prediction technology and research field advanced over the last 30 years. And the main reason AI based methods have been accepted and widely applied in biology. So shortsighted of NIH to postpone or even halt funding. John Moult is a scientific hero.
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John P. Overington @jpoverington.bsky.social · 01/07/2025
That's it. It's done. I am no longer on the other place. I'm going to miss some of the science on there, and in particular the biotech analyst community seems stuck there, but enough was enough. It had to go.
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John P. Overington @jpoverington.bsky.social · 01/07/2025
Is there anywhere online a free lexicon for alternate spelling of scientific terms between US and UK English. Something that contains the equivalence of sulphotransferase = sulfotransferase, protease = proteinase, etc. But also smart to know that synthase and synthetase are different concepts.
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John P. Overington @jpoverington.bsky.social · 01/07/2025
UI oddity of the day - a box to ask if I'm human, which looks like the only option I have is to click to say no, turns out it's a slider hiding as a tick box.
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John P. Overington @jpoverington.bsky.social · 14/06/2025
Waiting.
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John P. Overington @jpoverington.bsky.social · 14/06/2025
It’s my son’s birthday, so we are at a Metallica concert.
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John P. Overington @jpoverington.bsky.social · 06/06/2025
Anyone interested in some paid freelance writing on AI in drug discovery for drughunter.com - if so get in touch for more details !
drughunter.com
Drug Hunter - drug discovery, distilled
Drug Hunter is for drug discovery scientists who want to discover new ideas but don't have time to read everything.
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John P. Overington @jpoverington.bsky.social · 16/05/2025
This weeks questionable use of AlphaFold is is the prediction of the structure of a novel 12mer peptide BRP. www.nature.com/articles/s41...
nature.com
Prohormone cleavage prediction uncovers a non-incretin anti-obesity peptide - Nature
Computational drug discovery is used to identify a 12-mer peptide derived from BRINP2 with potent anti-obesity effects that are independent of leptin, glucagon-like peptide 1 receptor and melanocortin...
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John P. Overington @jpoverington.bsky.social · 09/05/2025
A long day ahead, flying back home from Hamburg via Munich. Really enjoyed the CSSB 2025 conference, learnt so much; realised how much I missed virology.
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John P. Overington @jpoverington.bsky.social · 07/05/2025
At DESY in Hamburg at CSSB for a few days. I’ll speak on structural biology and systems approaches in drug resistance, with a little splash of AI thrown in. I love these big science campuses.
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John P. Overington @jpoverington.bsky.social · 03/05/2025
I bought a really cute cactus today. Put it in plastic bag, then managed to enter glochid hell. Here is my hand with PVA glue waiting to dry.
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John P. Overington @jpoverington.bsky.social · 27/04/2025
The approval of new differentiated drugs that improve on current therapies and particularly the approval of novel drugs for currently untreated diseases are the heartbeat of progress of the pharmaceutical industry and improved human health.
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John P. Overington @jpoverington.bsky.social · 25/04/2025
…framing the narrative as being around the ‘poor exploited creators’, as opposed to media company profits is poor. Almost as biased as the ‘poor unrewarded destitute session musicians’ raised by music companies to extend copyright. #RantOver
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John P. Overington @jpoverington.bsky.social · 25/04/2025
Reading Nature magazine in the garden before work. What has happened to the rigour of writing. Why don’t editorials have a named author, piece on “will AI improve your life?” Naive analysis - just one minor point among many, on data concerns, creators mean nothing, its rights holders that count….
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John P. Overington @jpoverington.bsky.social · 24/04/2025
For the alpha folders out there - how much does alpha fold capture of the actual physics (aka reality) of protein folding. Imagine the thought exit, where you model a subsequence of a larger protein - trypsin for example - about 240 , if you took a subsequence of say 20 from this and modeled it...
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John P. Overington @jpoverington.bsky.social · 22/04/2025
The editorial about AI drug development’s data problem in Science Is a bit odd. Where was the 20-30% greater citations for open gene sequences come from? Then the highlighted AIRCHECK data set, turns out the compound structures aren’t open at all.
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John P. Overington @jpoverington.bsky.social · 20/04/2025
When I started my PhD at Birkbeck I shared an office with Alan Mackay. He was a truly wonderful person, I never told him that at the time. Just saw that he passed away earlier this year. en.m.wikipedia.org/wiki/Alan_Li... Sadly missed.
en.m.wikipedia.org
Alan Lindsay Mackay - Wikipedia
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Anshul Kundaje @anshulkundaje.bsky.social · 20/04/2025
genomebiology.biomedcentral.com/articles/10.... Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
genomebiology.biomedcentral.com
Zero-shot evaluation reveals limitations of single-cell foundation models - Genome Biology
Foundation models such as scGPT and Geneformer have not been rigorously evaluated in a setting where they are used without any further training (i.e., zero-shot). Understanding the performance of mode...
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John P. Overington @jpoverington.bsky.social · 19/04/2025
At the finals of the First 2025 Championship Robot competition. It’s huge!
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John P. Overington @jpoverington.bsky.social · 16/04/2025
Just reading some old literature on penicillin and toxicity, there's a great turn of phrase I don't think can be beaten in the discussion of SAR - from watermark.silverchair.com/postgradmedj...
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John P. Overington @jpoverington.bsky.social · 14/04/2025
Nice paper on transcript profiling in aging macaques - great to see data on more human-like systems than elegans and drosophila - lot's to digest from the patterns in this. Nice line in the paper 'meticulously shielded from all environmental factors except aging' www.nature.com/articles/s41...
nature.com
Transcriptome analysis of cynomolgus macaques throughout their lifespan reveals age-related immune patterns - npj Aging
npj Aging - Transcriptome analysis of cynomolgus macaques throughout their lifespan reveals age-related immune patterns
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John P. Overington @jpoverington.bsky.social · 12/04/2025
My first home grown pineapple is coming along well. I had no idea there were flowers though.
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John P. Overington @jpoverington.bsky.social · 10/04/2025
Another role - a data analyst - in my Data and informatics group at drughunter.com. drughunter.isolvedhire.com/jobs/1419540, position is remote, based in the US and open to candidates with right to employment in the US.
drughunter.com
Drug Hunter - drug discovery, distilled
Drug Hunter is for drug discovery scientists who want to discover new ideas but don't have time to read everything.
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John P. Overington @jpoverington.bsky.social · 05/04/2025
At a robot competition today with Albert. Great to see youngsters into STEM!
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John P. Overington @jpoverington.bsky.social · 01/04/2025
One thing I wish for is email systems that can handle attachments of reasonable size - PowerPoints rapidly grow above typical email attachment limits, and force sucking attachments into different cloud storage solutions.
differs.cloud
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Reposted by John P. Overington
Shicheng Guo @shihcheng.bsky.social · 28/03/2025
A cryptic pocket in CB1 allows creation of peripherally selective agonists. This strategy reduces central effects and tolerance, addressing opioid overdose concerns. PMID:40044849, Nature 2025, @Nature doi.org/10.1038/s41586-025-08618-7 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
doi.org
A cryptic pocket in CB1 drives peripheral and functional selectivity | Nature
The current opioid overdose epidemic highlights the urgent need to develop safer and more effective treatments for chronic pain1. Cannabinoid receptor type 1 (CB1) is a promising non-opioid target for pain relief, but its clinical use has been limited by centrally mediated psychoactivity and tolerance. We overcame both issues by designing peripherally restricted CB1 agonists that minimize arrestin recruitment. We achieved these goals by computationally designing positively charged derivatives of the potent CB1 agonist MDMB-Fubinaca2. We designed these ligands to occupy a cryptic pocket identified through molecular dynamics simulations—an extended binding pocket that opens rarely and leads to the conserved signalling residue D2.50 (ref. 3). We used structure determination, pharmacological assays and molecular dynamics simulations to verify the binding modes of these ligands and to determine the molecular mechanism by which they achieve this dampening of arrestin recruitment. Our lead li
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Keith Hornberger @krhornberger.bsky.social · 22/03/2025
J Med Chem is on 🔥 with the editorials lately, and I highly recommend giving this one a read. Understanding free drug principles is the gateway to all of pharmacology, and is all too often mangled and misapplied by drug discovery practitioners.
pubs.acs.org
Free Drug Concepts: A Lingering Problem in Drug Discovery
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