Peldom Zhang

3rd-year PhD candidate at #WestlakeUniversity majored in Computational Structural Biology, Protein designer, AIDD/CADD developer, Tech savvy, Amateur astronomer

[bioRxiv Synthetic Biology @bioRxiv_synbio]

De novo design of metalloproteases for targeted amyloid-β cleavage https://t.co/NJsVJgWuo6 #biorxiv_synbio

[Peldom Zhang @PeldomZ]

Latest publication of our lab! 🎉
Amantadine-controlled protein-designed assembly, as an ideal amantadine-inducible gene switch for therapeutic applications

[Biology+AI Daily @BiologyAIDaily]

De novo design of small molecule–regulated protein oligomers @ScienceMagazine

1. Researchers have developed a novel computational method to design protein oligomers regulated by small molecules, focusing on the FDA-approved drug amantadine. This approach enables precise control over protein assembly, offering potential applications in biotechnology and cell-based therapies.

2. The study introduces a "docking-while-binding" technique that simultaneously optimizes protein-protein and protein-ligand interactions. This method allows for the de novo creation of ligand binding pockets directly at the protein-protein interface, enabling the design of homotrimers, heterodimers, and heterotrimers.

3. The designed amantadine-regulated protein oligomers were validated in cellular and animal models, demonstrating their ability to control gene expression, protein localization, and reversible condensate formation. Notably, the system achieved noninvasive, dose-dependent control of gene expression in mice through oral administration of amantadine.

4. The compact size of the protein components (~65 amino acids) and the use of an orally bioavailable small molecule make this system highly suitable for translational applications. The approach opens new avenues for developing next-generation chemically inducible protein assembly tools.

5. The study highlights the potential for further optimization using deep learning models and the incorporation of additional ligands to enhance sensitivity. This work represents a significant advancement in the field of chemogenetics, providing a versatile toolkit for manipulating complex biological processes.

📜Paper: https://t.co/SYQuN3X34y
#ProteinDesign #Chemogenetics #SyntheticBiology #Biotechnology #GeneRegulation

[Peldom Zhang @PeldomZ]

"One method to design them all, and in the darkness bind them."
Introducing our lab's new unified #proteindesign method HalluDesign!
This lab-proven single approach lets us design universal binders (incl. antibodies/peptides) for: DNA/protein/ion/ligand

[Minchao Fang @minchaofang]

🚀 New Paper: We’ve just released HalluDesign – a novel framework for protein optimization and de novo design using AlphaFold3-style models, without finetuning or gradient backpropagation! 🎉

https://t.co/tmqKqPMp2b

[Peldom Zhang @PeldomZ]

Paper link: https://t.co/hxpNv2tR9H

[Peldom Zhang @PeldomZ]

Lastest paper of our Lab!🎉
Light-controlled de novo protein assemblies

[Life Science Journal Content @lsn_jc]

De novo design of light-responsive protein–protein interactions enables reversible formation of protein assemblies
#science #publication #research #journal
https://t.co/Hw3xcP16TT

[Peldom Zhang @PeldomZ]

@ChoYehlin @MartinPacesa @ZhidianZ @sokrypton How about the generation speed of BoltzDesign1?

[Peldom Zhang @PeldomZ]

A breakthrough in glioblastoma treatment! Qihan Jin of our lab, de novo designed binders on CAR-T cells to target tumor antigens. Remarkable results in mice, clinical trials are underway. #proteindesign #glioblastoma #CART
@lxcaosd
https://t.co/8wzr3KktsH

[Peldom Zhang @PeldomZ]

Witness of the history in protein design!

[The Nobel Prize @NobelPrize]

BREAKING NEWS
The Royal Swedish Academy of Sciences has decided to award the 2024 #NobelPrize in Chemistry with one half to David Baker “for computational protein design” and the other half jointly to Demis Hassabis and John M. Jumper “for protein structure prediction.”

[Peldom Zhang @PeldomZ]

@GoogleDeepMind Will the model be published?

[Peldom Zhang @PeldomZ]

@DdelAlamo That’s true, and followed by 1-2 rounds of SSM screening for optimizing Kd

[Peldom Zhang @PeldomZ]

Congratulations to Lu lab! D-binder design inspired by mirror biology.

https://t.co/z18JneSp0I

[Peldom Zhang @PeldomZ]

@LeoTZ03 Thanks! I'm honored for the share. Looking forward to continuing to contribute and learn from everyone.

[Peldom Zhang @PeldomZ]

@alexrives Why ESM3 didn't generate a helix-based GFP? or GFP with a different topological tim-berral structure?

[chentongwang @WChentong]

Glad to see our paper:Proteus: Exploring Protein Structure Generation for Enhanced Designability and Efficiency accepted by icml2024. Excited to witness the full potential that structure generation methods can achieve.
Paper:
https://t.co/v30lYExv2T
Code:
https://t.co/b6ns3TlOgy

[Peldom Zhang @PeldomZ]

@BioSpace9 Targeting TLR3 is so tricky. With a polar surface, it seems untargetable, hard to be expressed

[Peldom Zhang @PeldomZ]

@AilurusBio @opentrons Cool! We just label an 'I' for 'IPTG' randomly on EP tubes and throwing them somewhere in -20 fridge

[Peldom Zhang @PeldomZ]

🎉 Celebrating 1000 stars on our GitHub repository! 🌟 A repo for recording papers of Deep Learning for Protein Design. Join us in advancing computational biology! Check it out: https://t.co/QGofZj49Dd #DeepLearning #ProteinDesign

[Peldom Zhang @PeldomZ]

Congratulations to @WChentong ! Latest work of our lab

[Martin Pacesa @MartinPacesa]

New backbone diffusion model Proteus from Longxing Cao’s group, displaying better backbone self consistency than RFdiff and Chroma. Some experimental evidence presented as well.

https://t.co/Ge2aoAWsI0

[Peldom Zhang @PeldomZ]

@IsomorphicLabs @GoogleDeepMind What's the performance comparing another all-atom prediction model RoseTTAFold All-Atom(RFAA)?

[Peldom Zhang @PeldomZ]

@nob_mai @kobnaoya Interesting! We've generated similar backbones with our method before, but we thought those are bad backbones result in no protein expression(monomer aggregated before complex assembling), so they are abandoned. A great discovery and extension for knottins!