PhD student @TheSainsburyLab studying NLR bioengineering & computational prediction of immune receptor activities w/ @KamounLab. 🇦🇷🇮🇹🇦🇲🏳️🌈 views my own
Norwich, UK
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Excited to share Fold on Tight! 🎉
We distil recent advances in plant immunity into 10 lessons for using AI structure prediction critically and effectively, in plants and beyond.
With @amiralito_ Alex McClelland @YuSugiharaY @mpcontreras4 @KamounLab
📝zenodo.org/records/22100279
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Andy Posbe retweeted
LIVIA has a new intro video, made by Claude Opus 5.5 in Claude Code. When the biosafety filter stays quiet, Claude is quite nice.
Webtool: flyark.github.io/LIVIA/unive…
Preprint: doi.org/10.64898/2026.05.01.…
🚀 New tool out! LIVIA (Local Interaction Visualization and Analysis) — a browser-based tool for assessing and visualizing predicted protein-protein interactions.
Drop in a prediction from AlphaFold-Multimer, AF3, ColabFold, Boltz-1/2, Chai-1, or OpenFold3 (ZIP or folder, auto-detected) and LIVIA answers the two questions you actually care about:
▸ Do these proteins interact?
▸ Which residues form the interface?
What you get:
▸ Interface confidence scores — iLIS (our local metric), ipSAE, actifpTM, ipTM
▸ Interaction interface heatmaps (PAE, LIS, cLIS)
▸ Sequence viewer + linear & circular contact maps highlighting Local Interaction Residues (LIR) and contact LIR (cLIR)
▸ Embedded Mol* 3D viewer
▸ Downloadable ChimeraX & PyMOL scripts
Also fetches dimers directly from the AlphaFold Database — adding the interface annotations AFDB doesn't provide.
Everything runs locally in your browser. No install, no upload.
LIVIA started as a personal tool — I built it with Claude Code and used it to make every structure figure in our FlyPredictome preprint (Kim et al., 2026). (Claude Code is truly insane...) Along the way I realized it could be useful for others, too.
If you have a favorite color palette for structure visualization, please let me know — happy to add it as a preset 🎨
🔗 LIVIA tool: flyark.github.io/LIVIA
🐍 iLIS / batch CLI: github.com/flyark/AFM-LIS
📄 LIVIA preprint: biorxiv.org/content/10.64898…
📄 FlyPredictome preprint: biorxiv.org/content/10.64898…
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Andy Posbe retweeted
ʙɪɴᴅᴄʀᴀꜰᴛ2 now designs almost any binder format:
-mini & large binders
-linear & cyclic peptides
-VHHs, scFvs & Fabs
-ankyrin repeat proteins (ARPs)
-homo-oligomers & multidomain binders
-induced-fit & fold-switch binders
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Andy Posbe retweeted
We built a custom integrated engine that makes ʙɪɴᴅᴄʀᴀꜰᴛ2 dramatically faster than v1.
And it isn't limited to structured domains: you can target disordered regions, short linear motifs, or a target given as a bare sequence.
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Andy Posbe retweeted
Back from the @GetGenome workshop in Tunisia 🇹🇳. Initiatives like this have a huge impact on young scientists with limited resources. Deeply inspiring, Science shouldn't have borders!!!🚀💡Thanks for the invitation and the experience!
#DirectImpactScience
getgenome.net/
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Andy Posbe retweeted
Thank you, Javier, for joining us !! It was a real pleasure meeting you 🤩
Next challenge: mastering the Tunisian dialect… 😂😉
Back from the @GetGenome workshop in Tunisia 🇹🇳. Initiatives like this have a huge impact on young scientists with limited resources. Deeply inspiring, Science shouldn't have borders!!!🚀💡Thanks for the invitation and the experience!
#DirectImpactScience
getgenome.net/
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Andy Posbe retweeted
Two seemingly unrelated sides of our lab collided today in the AWESOME new Angiosperm Phylogeny Group system poster: flowers 🌸 and phylogenomics 🧬
Need a new genome? Just pick up the phone and “dial-a-genome” 📞🧬 @GetGenome
tudelft.nl/en/hortus-botanic…
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Andy Posbe retweeted
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/BindCra…
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Andy Posbe retweeted
More brik danouni…
Tunisia: an Argentinian dream?
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Andy Posbe retweeted
Happening now @EspaceZmorda 🇹🇳
AI in Genomics workshop!
@GetGenome @TheSainsburyLab on how AI can be used across genomics — from working with genomic data to protein structure prediction, biological discovery and developing new research questions.
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Andy Posbe retweeted
Brik danouni--ancestral state of empanadas...? 🇹🇳🇪🇸🇦🇷 elsursf.com/blogs/news/a-bri…
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Andy Posbe retweeted
Excited to share this pre-print from my PhD work! We explore a Pmk1-Mst12-Bip1 network required for appressorium-mediated infection by the blast fungus 🌾 biorxiv.org/content/10.6... Thread 👇
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Andy Posbe retweeted
We just published: Fold on Tight — 10 lessons on AI structure prediction
Andy Posbe @adnroide turned our ten lessons on AI structure prediction into a thread. Here it is, one lesson at a time.
kamounlab.medium.com/fold-on…
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Andy Posbe retweeted
Can I add a Lesson 11: don't use ipTM. It has artifacts when proteins have extra non-interacting domains or disordered regions. Use ipSAE or LIS which filter out the poor PAE regions and focus on the well predicted parts of the interaction.
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No one remembers authorising this firmware update.
ALT Five researchers hold freshly printed immune receptor structures while the office Ricoh continues production, despite nobody remembering authorising this feature.
Excited to share Fold on Tight! 🎉
We distil recent advances in plant immunity into 10 lessons for using AI structure prediction critically and effectively, in plants and beyond.
With @amiralito_ Alex McClelland @YuSugiharaY @mpcontreras4 @KamounLab
📝zenodo.org/records/22100279
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Andy Posbe retweeted
This project has been a labor of love and grateful for my supervisor @YuSugiharaY's guidance every step of the way 🌱🙏
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Andy Posbe retweeted
#ProudSupervisor moment 🥲 Congrats @mai_garro for winning best poster prize at @BS_PP 2026! It was an honor to work with you and @amiralito_ during your predoc with @KamounLab!
All the best in your new adventures in the @JohnInnesCentre Rotation PhD programme 💪💪💪
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Excited to share Fold on Tight! 🎉
We distil recent advances in plant immunity into 10 lessons for using AI structure prediction critically and effectively, in plants and beyond.
With @amiralito_ Alex McClelland @YuSugiharaY @mpcontreras4 @KamounLab
📝zenodo.org/records/22100279
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RoseTTAFold All-Atom: github.com/baker-laboratory/…
RF3: github.com/RosettaCommons/fo…
ESMFold: github.com/facebookresearch/…
ESMFold2: github.com/Biohub/esm
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Interface confidence scores
ipSAE: github.com/DunbrackLab/IPSAE
pDockQ: gitlab.com/ElofssonLab/FoldD…
LIS: github.com/flyark/AFM-LIS
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