Brady Johnston retweeted
My @SocDevBio Sci-Comm Award Lecture is online!
Here I tell my story of getting into art in the lab 🔬:
youtu.be/jxu82LkpNqU?si…
Here I tell my story of getting into art in the lab 🔬:
youtu.be/jxu82LkpNqU?si…
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Brady Johnston retweeted
Finished making a system of DNA cutting and ligation in Molecular Nodes, made to be non-destructive. Allows mutiple cut sites and RE's. Example is a Pst1 site.
Did this so I can do more DNA stuff in the future :)
Made in #Blender with #MolecularNodes
Did this so I can do more DNA stuff in the future :)
Made in #Blender with #MolecularNodes
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Brady Johnston retweeted
slightly different colored stills
Finally got GROMACS molecular dynamics simulations live-streaming directly into Blender using Molecular Nodes! Done via Docker, IMDv3
1.44 picoseconds/72 frames, all-atom molecular dynamics simulation of lysozyme in water, 303.15 K/30°C
#GROMACS #Blender3D #MolecularDynamics #MolecularNodes
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Brady Johnston retweeted
Underrated contribution to the AI for proteins explosion.
My little Blender plugin I started 4.5 years ago is literally the face of an entire Biotech industry / research sector 🥹
#b3d #GeometryNodes #MolecularNodes
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Brady Johnston retweeted
Protein design doesn’t have to stop at the canonical 20 amino acids! After our work on phosphotyrosine binders, RFD4-Proteina adds phosphoserine and phosphothreonine (below) to the repertoire, with binders that distinguish adjacent H3pS10 and H3pT11 sites in the histone H3 tail!
@ArashVahdat @karsten_kreis @tomasgeffner @nscorley @RafiBrent @maxkazman @osclsd @nmboffi @ChoYehlin @jBonzaniniSci @noramcb The unified latent space pushes specificity further: with @kinasekid we bind phosphorylated serines and threonines specifically, and even site-selectively when they sit directly next to each other on a target! 22/30
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Brady Johnston retweeted
DAY 29 / 100 🧬
Built a ferritin figure showing the 24-mer nanocage, hollow cavity, and three-fold channel. I used cutaway and selective emphasis to make the structural hierarchy easier to read.
#Blender #SciViz #SciArt #b3d #MolecularVisualization
Built a ferritin figure showing the 24-mer nanocage, hollow cavity, and three-fold channel. I used cutaway and selective emphasis to make the structural hierarchy easier to read.
#Blender #SciViz #SciArt #b3d #MolecularVisualization
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Brady Johnston retweeted
DAY 28 / 100 🧬
Explored surface representation for proteins and tested selective emphasis by muting most chains while keeping one highlighted. It was a useful way to control where the viewer looks first.
#Blender #SciViz #b3d #MolecularVisualization
Explored surface representation for proteins and tested selective emphasis by muting most chains while keeping one highlighted. It was a useful way to control where the viewer looks first.
#Blender #SciViz #b3d #MolecularVisualization
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Brady Johnston retweeted
Huge thanks to @bradyajohnston for #MolecularNodes! Such a fantastic tool for bringing our protein designs to life and making the science easier to share. Super visionary to build it! 🙌
My little Blender plugin I started 4.5 years ago is literally the face of an entire Biotech industry / research sector 🥹
#b3d #GeometryNodes #MolecularNodes
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Brady Johnston retweeted
Remember seeing the first 3 videos of @bradyajohnston on YouTube and joining a Zoom meeting Australian time at an ungodly hour for Europe to learn this wizardry he was preaching. Fast forward today and MolecularNodes is well-deserved the tool of choice for me and many others!
My little Blender plugin I started 4.5 years ago is literally the face of an entire Biotech industry / research sector 🥹
#b3d #GeometryNodes #MolecularNodes
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My little Blender plugin I started 4.5 years ago is literally the face of an entire Biotech industry / research sector 🥹
#b3d #GeometryNodes #MolecularNodes
#b3d #GeometryNodes #MolecularNodes
Avengers assemble: 1 year BakerLab + NVIDIA GenAIR = 🔥 rfd4-proteina.org
Presenting RFD4-Proteina, our latest protein design model, significantly better and faster than everything we compared against, both in silico and in the lab! 1/30
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Brady Johnston retweeted
BindCraft2 v1.0.4 has been released: with significantly improved VHH, scFv, ARP, and induced fit targeting. WE also improved speed and code stability. Try your difficult campaigns again. Great work by Erik Mäeots, Leonardo Tredese and Elizaveta Chernova.
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Brady Johnston retweeted
quick render of Apaf-1 apoptosome (pink is cytochrome C, rest is Apaf-1)
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Brady Johnston retweeted
I made an animated horror short! It's called Monitor. I did everything myself (except the awesome music and sound). No AI. Hope you enjoy!
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Brady Johnston retweeted
DAY 26 / 100 🧬
Built a hierarchical figure of human deoxyhemoglobin, moving from the α₂β₂ tetramer to a β-globin subunit and the heme group. Focused on keeping the three-panel hierarchy clear.
#Blender #SciViz #ScientificVisualization #MolecularVisualization
Built a hierarchical figure of human deoxyhemoglobin, moving from the α₂β₂ tetramer to a β-globin subunit and the heme group. Focused on keeping the three-panel hierarchy clear.
#Blender #SciViz #ScientificVisualization #MolecularVisualization
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Brady Johnston retweeted
of course that's your contention. you're a first-year frontier bio guy. you just finished reading about CRISPR, probably watched a Doudna talk too. so now you're convinced everything is just gene editing.
that's gonna last until next month when you discover base editing, and lkin' about how cutting DNA was barbaric and double-strand breaks are a legacy approach.
then you're gonna read about delivery, and suddenly everything's about lipid nanoparticles and how editing was the easy part and the whole goddamn thing is bottlenecked by getting it to the right organ.
that'll last until somebody shows you AlphaFold, and then you're gonna be in here regurgitating DeepMind, talkin' about de novo enzymes and virtual cells and how wet labs are economically obsolete.
then six months from now you'll watch one assay fail four times in a real lab, and start telling everybody the bottleneck was never ideas, it's validation.
somewhere in there you'll find a guy named Keith on Telegram, and you'll start doing reconstitution math in your head at dinner.
and by next year you're gonna be standing right here explaining to me you reversed your biological age by six years because you picked the clock that said so.
that's gonna last until next month when you discover base editing, and lkin' about how cutting DNA was barbaric and double-strand breaks are a legacy approach.
then you're gonna read about delivery, and suddenly everything's about lipid nanoparticles and how editing was the easy part and the whole goddamn thing is bottlenecked by getting it to the right organ.
that'll last until somebody shows you AlphaFold, and then you're gonna be in here regurgitating DeepMind, talkin' about de novo enzymes and virtual cells and how wet labs are economically obsolete.
then six months from now you'll watch one assay fail four times in a real lab, and start telling everybody the bottleneck was never ideas, it's validation.
somewhere in there you'll find a guy named Keith on Telegram, and you'll start doing reconstitution math in your head at dinner.
and by next year you're gonna be standing right here explaining to me you reversed your biological age by six years because you picked the clock that said so.
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Brady Johnston retweeted
Bacteria have immune systems to defend against their viruses.
This animation shows the proposed mechanism of the Zorya defense system from our work with @NMITaylorLab: a proton-driven membrane complex related to the bacterial flagellar stator.
doi.org/10.1038/s41586…
This animation shows the proposed mechanism of the Zorya defense system from our work with @NMITaylorLab: a proton-driven membrane complex related to the bacterial flagellar stator.
doi.org/10.1038/s41586…
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Brady Johnston retweeted
How do bacteria build their flagella?
We’ve put together an animation of Salmonella flagellum assembly based on cryo-EM and X-ray structures.
From the membrane-embedded machinery to the growing filament, here’s how the parts come together, step-by-step.
We’ve put together an animation of Salmonella flagellum assembly based on cryo-EM and X-ray structures.
From the membrane-embedded machinery to the growing filament, here’s how the parts come together, step-by-step.
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Brady Johnston retweeted
used @bradyajohnston nodebpy to migrate the source of truth for all 140 nodes in my toolkit from a .blend file to actual human readable python code :) such a great python package
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