Jim Horne

@AdrianoAguzzi Why do you think higher glycerol is worse? My hypothesis would of been it is a better cryoprotectant

@SujeetKumar_LSU Cool results, I was asking @Figlegend about this very question last week!

New paper from @SujeetKumar_LSU and co, finally finding the OM clamp for one of the non-TamB AsmA-like proteins! If we could just do all vs. all cell envelope proteins in AF2 I wonder what else we would discover pnas.org/doi/full/10.10…

@maru_to_y 私も!

AlphaFold3のHPにのってるのWD40 repeatじゃん BamBで頭がいっぱいだからか、おっ！となった

This is insanely cool. Rendering protein/cell scenes and tomograms using Unreal Engine 5 so you can display more with less GPU overheads and control a character to fly through them! biorxiv.org/content/10.110…

More than proud to see our work on SlyB out in press @Nature! Who would have thought a small membrane protein could form protective nanodiscs. A big thank you to all collaborators and reviewers. Find out more: nature.com/articles/s4158…

@4rtsy2wo @martinmbauer *postdocs are sub 4-years

@4rtsy2wo @martinmbauer Most postdocs across the UK including Oxbridge (except London) won't pass the threshold until at least postdoc year 3-4. I would suspect that >50% of all postdocs have are sub 4-years. So it would cover the vast majority of them

I hope the prime minister is aware that salaries of postdoctoral researchers have reached such a low level in this country that this law would make it impossible for UK scientists to employ international experts It would be a huge own goal!

@KyrieGrasekamp @NatureComms @ChrisBel70 @SGribaldo @BasileBeaud Very cool stuff

Our new paper is out in @NatureComms! The Mla system, but not as we know it: looks like the 6-protein pathway in E. coli is an exception, not a rule... Thank you to all our collaborators and reviewers:) @ChrisBel70 @SGribaldo @BasileBeaud nature.com/articles/s4146…

Glad to see this paper from Sam finally out with tons of very cool in vivo fluorescent labelling tricks!

@ATinyGreenCell That was fun! Thanks for sharing

Biology is hard. Nothing works the first try. Being careful is obviously paramount. The most important part of this practice is to never give up. Trust nothing, question everything, and never give up. Ad astra. 34/34 end of thread

I have failed...but I couldn't be happier. A small thread on recent experiments 🧬🔀🧵 1/n

@sokrypton @g_pavlopoulos @BSRC_Fleming @kyrpides @jgi @SiruiLiu_ @UWproteindesign Very cool! I wonder if we can now visualise effectively 100% coverage for natural fold space or whether there are more hidden (to science) clades with many totally novel folds.

Exciting to see this finally out. We started this project ~7 years ago 🫣 @g_pavlopoulos @BSRC_Fleming @kyrpides @jgi @SiruiLiu_ @UWproteindesign (and twitterless Fotis!) nature.com/articles/s4158…

@xlinkx_pd @Chimera I've used this and it was very helpful! Was anything new added or just fixes?

We updated XMAS in @Chimera. There were a ton of requests and bug reports we dove into and all seems pretty much solved. If you're doing crosslinking and are aiming to model your way to a solution, give it a spin :). Shout out to Micha Birklbauer for committing a fix!

We're excited to share new tools, using photo-crosslinking mass spec 💡⚔️⚖️ to study protein structures and complexes in situ with high spatial and temporal resolution. Out now in @AmerChemSociety @an_chem. Short 🧵 1/8 pubs.acs.org/doi/10.1021/ac…

@bradyajohnston When are you talking in Cambridge?

Preparing some videos for upcoming talks. I'll be in Aarhus and Cambridge in the next couple of weeks. Lots of talking about EM data inside of #blender3d using #MolecularNodes and #GeometryNodes to create clear visuals and beautiful animations. Feels cool to zoom around a cell

@ATinyGreenCell Depending on how long you ran it for, I wonder if you would eventually select for a reduced lag phase?

Here's a fun question: I replicated one of Monod's PhD thesis experiments using E. coli K-12 to demonstrate a diauxic shift using mannitol and sorbitol in a batch culture. What would happen if the same media were to run in a turbidostat? Multiple catabolic repression curves?

Our new paper published in @jbiolchem. Categorization of Escherichia coli Outer Membrane Proteins by Dependence on Accessory Proteins of the β-barrel Assembly Machinery Complex jbc.org/article/S0021-…

In our just accepted paper in @angew_chem with @RadfordLab & @naranson in @AstburyCentre we used In-Cell PELDOR/DEER complemented by CryoEM to show the BAM complex adopts a lateral closed conformation in E coli cells in presence of antibiotic darobactin-B: onlinelibrary.wiley.com/doi/10.1002/an…

@michael_nielsen I don't if you have to completely retrain from scratch or if you can just update it by learning from mistakes. If it's a case of retraining it will be interesting to see what companies deem too expensive for a set return (is $1m for 5% better worth it?).

@_JimHorne Also, my sense is that (of course) it sometimes is getting structures wrong - but people are learning from this, and improving the systems in response.

A naive question: I'm trying to understand in what sense AlphaFold 2's protein structure predictions are *verifiable* A nice thing AF2 does is predict not just structure, but of how confident it is in that structure. Eg, blue in regions of high confidence, red in lower

@michael_nielsen As you point out though, AF2 can give you local confidence measures which is in some ways even better than experimental work. We often fool ourselves that proteins are fixed constructs (XRC and EM just give a snapshot). In reality they can be dynamic and part of an ensemble. 3/3

@michael_nielsen I think you've got the answer in your thread pretty well. This is a predictive algorithm. Something of this accuracy has until recently been very rare for biology but physics has tons of equations that allow you to predict the outcome before doing the experiment. 1/n