Johnson Samuel

PhD @MonashUni • Alumnus @iitdelhi, @NImmunology, @official_IBAB • Structural Virology 🧬 • #Poxvirus 🦠 • #CryoEM ❄🔬 • Photography 📸 • Cook 👨‍🍳

[Johnson Samuel @Johnson_Samuel_]

It was nice giving a talk to the #undergrad & #pregrad students at NMKRV college, Bengaluru, on various aspects of #structuralbiology & #cryoEM

#AcademicTwitter @VoicesofIndAcad @PhDVoice

[Weights & Biases @wandb]

.@SGRodriques left physics because "there were no unsolved problems left."

So he built an AI scientist to cure every disease, solve aging, & map the human brain.

New Gradient Dissent episode out now.

@l2k

[bioRxiv Microbiology @biorxiv_micrbio]

High-stability, clamp-free soluble Sarbecovirus spike trimers and their potential for pan-Sarbecovirus vaccine development. https://t.co/XRAMKHF2Yd #biorxiv_micrbio

[Johnson Samuel @Johnson_Samuel_]

🚨Preprint alert🚨

- The preprint of our work on pan-coronavirus vaccine development study is out now in @biorxivpreprint

- We establish a framework for producing stable & highly immunogenic S subunit vaccine

https://t.co/Yti9uwT3hq

@PhDVoice @AcademicChatter @OpenAcademics

[Judit Penzes @judit_penzes]

Although parvoviruses are relatively structurally well-characterized, the virion structure and morphology of chapparvoviruses were unknown. Today, we published the first capsid structure of these elusive viruses in @VirusesMDPI
https://t.co/t3YH3aBiEB

[Structura Biotechnology @structurabio]

Grappling with poorly-resolved ligand binding sites in #cryoEM maps?
Check out our new case study on a peptide ligand-bound GPCR showing how practical tips and features in #CryoSPARC v4.7 improve locally refined map quality & reveal clearer ligand density!
https://t.co/bGHWwbEu7O

[Colossal Biosciences® @colossal]

We’re Colossal Biosciences, the de-extinction company responsible for bringing back the first animals from extinction. Our dire wolf pups, Romulus and Remus, were born on October 1, 2024. Watch these pups grow up on our YouTube channel. Link in bio.

These two wolves were returned from extinction using genetic edits derived from a complete dire wolf genome, meticulously reconstructed from ancient DNA found in fossils dating back 11,500 and 72,000 years. This achievement is the result of years of pioneering science, tireless innovation, and unwavering dedication.

It marks a major milestone not only for our company, but for science, conservation, and humanity. With the birth of Romulus and Remus, de-extinction is no longer theory—it’s reality. There’s more work ahead, but this moment redefines what’s possible for the planet’s future.

[Fagan Lab at the University of Sheffield @RobFagan]

New paper alert 🚨 We've solved the complete structure of a C. difficile-infecting phage using cryo-EM, in both extended and contracted conformations - published today in Life Science Alliance

[Julia Bauman @JuliaBauman2]

As promised, an overview of @Roche 's new sequencing tech.

Comparable to Illumina NGS in accuracy & read length, but FAST - 5B reads in an hour!

[Kathy Y. Wei, Ph.D. @KathyYWei1]

It's pretty hard to beat AI cat video cuteness, but here goes 😆

[Biology+AI Daily @BiologyAIDaily]

What does AlphaFold3 learn about antigen and nanobody docking, and what remains unsolved?

The article investigates the performance of AlphaFold3 (AF3) in the context of antibody and nanobody docking with antigens, focusing on its successes and areas requiring further improvement.

1/ The study compares AF3’s performance with previous methods, showing a significant increase in the high-accuracy docking success rate for both antibodies (11.0%) and nanobodies (11.4%) when compared to AlphaFold2-Multimer and AlphaRED.

2/ AF3 achieves notable success in predicting antibody and nanobody structures, with CDR H3 loop accuracy playing a crucial role. The accuracy of this loop directly impacts the docking success, with sub-angstrom CDR H3 RMSD correlating strongly with correct docking.

3/ While AF3 improves docking quality, its single-seed failure rate remains at 60%. The article emphasizes that additional seed sampling can help overcome this limitation, with AF3 achieving a 60% success rate when 1,000 seeds are used.

4/ Antigen context is found to enhance the prediction accuracy of CDR H3 loops. The study shows that providing antigen context during AF3 predictions leads to better modeling of both the shape and placement of the antibody's CDR H3 loop.

5/ The authors discuss the optimization of confidence metrics, combining I-pLDDT and ΔGB to improve discrimination between correct and incorrect complexes. This method increases the accuracy of predictions when combined with energy calculations from Rosetta.

6/ AF3’s advancements demonstrate its potential for accelerating antibody engineering, although further refinement is needed. The study’s findings indicate that while AF3’s predictions are promising, a 60% failure rate for docking with single-seed sampling suggests room for improvement.

@jeffreyjgray
💻Code: https://t.co/IOmCk6ggV2
📜Paper: https://t.co/PpOlvt8nyb

#AlphaFold3 #AntibodyDocking #NanobodyDocking #ProteinModeling #Biophysics #MachineLearning #ComputationalBiology

[European Virus Bioinformatics Center @EVirusBioinfC]

The #ICTV has ratified extensive changes to #VirusTaxonomy, adding a new phylum and thousands of new taxa.

📄 https://t.co/nFptIxz7df
EVBC👤: @EvelienAdri, P. Alfenas-Zerbini, @BEDutilh, @judit_penzes @VandammeAm

[Johnson Samuel @Johnson_Samuel_]

@SuhagKirti Congratulations Kirti!!

[Daniel Hurdiss @DanielHurdiss]

I’m looking for a postdoc to join my team under a recently funded ERC Starting Grant.

If you’re passionate about structural #virology and have experience in #cryoEM SPA and/or #cryoET, get in touch!

Deadline: January 19th.

Please share 🙏

https://t.co/K3nFfjYIgA

[Bronte Johnstone @bronteaj]

Just in time for Christmas, our paper on the structure and evolution of baculoviruses is out! Excited to share some work I did at Monash in the @CoulibalyLab, with shout outs to co-authors @joshuamhardy and Jungmin, collaborators Mart and team and everyone else who contributed!

[Helena J. Shepherd 🇪🇺 @H_J_Shepherd]

The students are having fun in the teaching labs on the last day of term

[Kresten Lindorff-Larsen @LindorffLarsen]

📣 Save the dates 📅

We are organizing a Benzon Symposium on "Protein structure prediction and design" with what I think is an amazing set of speakers

Meeting will take place in Copenhagen 🇩🇰 on Sept. 1–4, 2025, and abstract submission will open in March

[Ellen Zhong @ZhongingAlong]

🚨New paper at #NeurIPS2024! We present Hydra, a mixture of neural fields 🐉🐉🐉 for ab initio cryo-EM reconstruction of complex mixtures.

Hydra is our attempt at pushing the boundaries for even more extreme forms of heterogeneity in cryo-EM 🤯.

This was joint work with an awesome team, led by @axlevy0 @rishwanth_raghu & David Shustin.

Paper: https://t.co/uHeaOezyqU
Poster session happening now! Come by 👋

[Johnson Samuel @Johnson_Samuel_]

@m_utkarsha_ @InBixAdnat2024 Congrats Utkarsha ba! 🎉

[I Am Dr. Sam 👩‍🔬 @SamanthaKDavis1]

Did you know there are viruses big enough to have their own viruses? Chantel Abergel went back to the land of dinosaurs by sampling permafrost to discover many weird and wonderful giant viruses 🤯 #AVS12 #virology @AusVirologySoc

[Ebony Monson, PhD @ebony_monson]

What a great first day of #AVS12! I'm really looking forward to hearing some great virology science over the next couple of days! @AusVirologySoc