#ProteinDesign
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djosergenomics.github.io
Part of HTGAA Week 4 is to write a proposal on an In-silico Bacteriophage Engineering.

My proposal: 'ArmoredPhage' 🛡️

My goal: Engineer a Thermostable MS2 Bacteriophage Using Protein Design Techniques.

Check it out:
djosergenomics.github.io/Armored-Phag...

#HTGAA #synbio #AlphaFold #proteindesign
A Schematic Showing a Brief Overview of the Proposed Pipeline PyMOL Visualization showing the full icosahedral 'shell' of the MS2 bacteriophage (PDB: 2MS2). PyMOL Visualization showing a single 'monomer' or 'building block' of the MS2 capsid protein. (Yellow is Beta Sheets, Red is Alpha helices, Green is in between loops)
November 11, 2025 at 5:21 PM
djosergenomics.github.io
Week 4 of HTGAA (Protein Design) is done & I'm amazed!

I was always intimidated by 3D protein models in papers & never thought I'd understand them one day!

Today, I loaded a PDB file into PyMOL, saw the alpha helices & beta sheets of my Tyrosinase enzyme.

This is so cool. 🚀
#HTGAA #proteindesign
PyMOL Visualization of Structures of Tyrosinase Enzyme (Red Alpha Helices, Yellow Beta Sheets, Green In between Loops) (PDB ID: 3NM8) PyMOL Visualization of Active Sites of Tyrosinase (Copper (II) ions in Orange) - Transparency = 0.35 (PDB ID: 3NM8)
November 11, 2025 at 2:27 AM
ing.dk
AI strukturerer data og finder ny mønstre. AI finder løsninger, vores hjerner ikke får øje på. Lige nu bringer AI forudsigelser på en lang række felter. Hør om de kollossale spring, AI leverer i meterologi, proteindesign og vedligeholdelse af skibsmotorer.
AI forudsiger det hele - vejret, proteinerne og olien i skibsmotorerne | Ingeniøren
AI strukturerer data og finder ny mønstre. AI finder løsninger, vores hjerner ikke får øje på. Lige nu bringer AI forudsigelser på en lang række felter. Hør om de kollossale spring, AI leverer i…
ing.dk
November 10, 2025 at 10:30 AM
alexis-verger.cpesr.fr
#proteindesign #proteinbinder

100 designs
⬇️
34 got through the screening (ipTM, PAE, RMSD)
⬇️
4 ordered (gene synthesis + codon optimization)
⬇️
3 expressed and soluble
⬇️
1 interacts with its target !!!!

Now the story begins !
a man with glasses and a mustache is wearing a white shirt and says yes .
ALT: a man with glasses and a mustache is wearing a white shirt and says yes .
media.tenor.com
November 7, 2025 at 12:03 PM
akhmelinlab.bsky.social
🚨 Registration open!
Join us next April on the Belgian coast 🇧🇪 for the FEBS Advanced Course “Generative AI for Protein Engineering” 🧬
A unique, hands-on week dedicated to thinking and designing like a protein engineer.

👉 Info & apply: …proteinengineering2026.febsevents.org
#ProteinDesign
November 5, 2025 at 5:43 PM
alexis-verger.cpesr.fr
#proteindesign #proteinbinder

😀

Now time to see if it binds what it is supposed to bind 🫣
November 5, 2025 at 11:47 AM
arxivlens.bsky.social
MolChord: Structure-Sequence Alignment for Protein-Guided Drug Design
Peiran Jin, Shufang Xie et al.
Paper
Details
#ProteinDesign #DrugDiscovery #MolChordStudy
November 4, 2025 at 5:13 PM
hlouchova-lab.bsky.social
Can proteins fold and function with half of the amino acid alphabet?
Using only 10 residues, we designed stable, mutation-resilient structures—no aromatics or basics involved.
A minimalist foundation for ancient biology and synthetic design. tinyurl.com/37t8br4v
#ProteinDesign #OriginsOfLife
Ancient amino acid sets enable stable protein folds
Early proteins likely arose from a chemically limited set of amino acids available through prebiotic chemistry, raising a central question in molecular evolution: could such primitive compositions yie...
tinyurl.com
November 3, 2025 at 4:48 PM
arstechni.ca
Neural network finds an enzyme that can break down polyurethane https://arstechni.ca... #neuralnetworks #proteindesign #biochemistry #polyurethane #chemistry #polymers #proteins #Science #Biology #enzymes #AI
October 31, 2025 at 11:59 PM
nilimesh.bsky.social
You don't need all 20 amino acids to build proteins! Here, authors showed
a reduced 10-amino-acid alphabet form exceptionally stable and resistant to mutations proteins!!
A key insight into the #OriginOfLife and a new foundation for minimalist #ProteinDesign.

www.biorxiv.org/content/10.1...
Ancient amino acid sets enable stable protein folds
Early proteins likely arose from a chemically limited set of amino acids available through prebiotic chemistry, raising a central question in molecular evolution: could such primitive compositions yie...
www.biorxiv.org
October 31, 2025 at 6:53 AM
alexis-verger.cpesr.fr
This week, I am trying to express proteins that do not exist #proteindesign #proteinbinder

How crazy is this?
October 29, 2025 at 1:14 PM
tum.de
Our university established professorships in #Marketing & Technology and #AI -guided #ProteinDesign, supported by the Wübben Stiftung Wissenschaft. The professorships were appointed to David Finken and Thomas Schlichthärle (pictured): go.tum.de/670372

📷A.Eckert
New endowed professorships for marketing and protein design
With the support of the Wübben Stiftung, TUM has established a professorship for Marketing & Technology and a professorship for AI-guided Protein Design.
go.tum.de
October 28, 2025 at 3:06 PM
csbj.org
🔗 AlphaFold3 prediction of protein-protein complex: Is it ready for thermodynamic analysis?. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.cs...

📚 CSBJ: www.csbj.org

#AlphaFold3 #ProteinDesign #MolecularModeling #ComputationalBiology #StructuralBiology #Thermodynamics
AlphaFold3 prediction of protein-protein complex: Is it ready for thermodynamic analysis?. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.015
October 19, 2025 at 8:08 PM
biosofttau.bsky.social
🌟 Upcoming #BioSoftSeminar 🌟
Join us Sun, Oct 19 | 16:00 | TAU (Kaplun 118)

Explore how self-assembling peptides & the QTY code are reshaping biomolecular design with Prof. Shuguang Zhang (MIT).

🧬 Where chemistry meets innovation!

#ProteinDesign #QTYCode #BiotechInnovation
October 16, 2025 at 7:02 AM
eunheechoilab.bsky.social
Proud collaboration with the Baker Lab (UW) and Bai Lab (UTSW).
#ProteinDesign #InsulinReceptor #MolecularCell #BiasedAgonism #TranslationalScience
October 14, 2025 at 2:10 AM
getnews-me.bsky.social
In October 2025 researchers introduced zero‑shot protein scaffolding using diffusion model Genie and Monte Carlo correction, enabling motif design without task‑specific training. Read more: https://getnews.me/zero-shot-protein-motif-scaffolding-with-diffusion-sampling-and-smc/ #proteindesign #smc
Zero‑Shot Protein Motif Scaffolding with Diffusion Sampling and SMC
October 6, 2025 at 5:09 PM
getnews-me.bsky.social
Score distillation cuts protein backbone generation to few steps, delivering over 20‑fold speedup while preserving designability comparable to the Proteina teacher model. https://getnews.me/score-distillation-cuts-protein-backbone-generation-time-over-20-fold/ #proteindesign #scoredistillation #ai
Score Distillation Cuts Protein Backbone Generation Time Over 20‑Fold
October 6, 2025 at 10:06 AM
getnews-me.bsky.social
RL with protein language models boosted success rates on four tasks—e.g., antimicrobial peptides and antibody design—while cutting the number of sequences sampled. Read more: https://getnews.me/reinforcement-learning-boosts-protein-language-models-for-design/ #reinforcementlearning #proteindesign
Reinforcement Learning Boosts Protein Language Models for Design
October 3, 2025 at 9:09 PM
arstechni.ca
Do AI-designed proteins create a biosecurity vulnerability? https://arstechni.ca... #riskassessment #proteindesign #bioterrorism #biohazards #security #Science #AI
October 3, 2025 at 9:00 PM
sbgrid.bsky.social
@caltech.edu doctoral student Vida Robertson highlighted a publication from Jens Meiler, from @vanderbilt.edu, who describes using Rosetta to design antibiotic peptides called lanthipeptides with antibiotic properties.

Read more here: buff.ly/d6k8HvB

#SBGrid #NMR #ProteinDesign
Investigating antibiotic characteristics from the computer
SBGrid member Jens Meiler uses Rosetta to design antibiotic peptides called lanthipeptides with antibiotic properties.
buff.ly
October 3, 2025 at 4:03 PM
purescience.news
AI-designed proteins test biosecurity safeguards #Science #Biology #MolecularBiology #Biosecurity #ProteinDesign #ArtificialIntelligence
AI-designed proteins test biosecurity safeguards
AI edits to the blueprints for known toxins can evade detection. Researchers are improving filters to catch these rare biosecurity threats.
purescience.news
October 3, 2025 at 12:27 AM
asbmb.bsky.social
#ASBMB26's keynote speaker is Wesley Sundquist: Co-chair of the department of biochemistry at @uofubiochem.bsky.social, ASBMB fellow and one of Time's 100 most influential people of 2025. Don't miss his speech at ASBMB 2026!
ow.ly/SxoY50X454R
#HIV #StructuralBiology #ProteinDesign
Text reads Keynote Speaker Wesley Sundquist, Professor and department of biochemistry co-chair, University of Utah. There is a photo of Sundquist and the background is a scientific image behind a blue, pink and orange gradient.
September 30, 2025 at 12:30 PM
joshuamhardy.bsky.social
I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5)
doi.org/10.1101/2025.09.24.678028 #proteindesign
ProteinDJ logo
September 28, 2025 at 9:16 PM
ismaelmingarro.bsky.social
#ProteinDesign #Apoptosis
Computacional design of potent and selective binders of BAK and BAX
www.science.org/doi/10.1126/...
Computational design of potent and selective binders of BAK and BAX
Selectively targeting BAK or BAX with potent designed proteins gives differential functional outcomes that inform therapy design.
www.science.org
September 25, 2025 at 4:23 PM
akhmelinlab.bsky.social
A little late to share 📸 but here’s a summer highlight — our REU intern Khuong Pham presented his poster at #RosettaCon2025 in Seattle 🌞 Super proud of his work!

Also a few snaps from the conference itself ✨

#ProteinDesign #RosettaCon25
September 23, 2025 at 8:50 AM