Minchao Fang

Westlake University ph.D. student

[Minchao Fang @minchaofang]

We are exploring optimal computational metrics for design selection and experimentally characterizing designed aptamers to advance structural-level nucleic acid design. Check out our preprint here: https://t.co/wst3V54EAZ

[Minchao Fang @minchaofang]

We are excited to announce that HalluDesign-NA is now available on GitHub: https://t.co/zeiu328ft9
We have expanded the HalluDesign framework to nucleic acids, enabling de novo design of nucleic acids by leveraging the hallucination ability of AF3-like models.

[Minchao Fang @minchaofang]

Within HalluDesign-NA, we are able to design large ssDNA/ssRNA monomers and dimers with diverse topologies and high confidence, as well as aptamers.

[澪乃ゆい@バイオインフォVTuber🧪🖥💊 @mionoyui]

低スループット条件で機能性核酸をde novo設計する枠組みはタンパク質設計ほど確立していませんが既存のHalluDesignを核酸向けに拡張し、NA-MPNNとAF3/Protenixを組み合わせた反復的な配列-構造共最適化で、ssDNA、ssRNA、DNA アプタマーを設計できるHalluDesign_NAが提案されました

ソースはリプ🔽

[Ah-Ram Kim @ahramkim1128]

HalluDesign-NA: Extending HalluDesign for De Novo Nucleic Acid Design https://t.co/gXrrKWB9sQ

[Minchao Fang @minchaofang]

We hope this direction will continue to grow and become even stronger with the community.

[Minchao Fang @minchaofang]

We are excited to announce that HalluDesign, an all-atom protein optimization and design platform, is now open-sourced and we have also updated our preprint:

https://t.co/tvzThrZBg9

https://t.co/BHRAzavb5O

[Minchao Fang @minchaofang]

The new version includes more detailed benchmarks and our newly developed ssRNA binders.

In addition, we are actively exploring other applications, including nanobody binding affinity optimization and cyclic peptide design.

[Peldom Zhang @PeldomZ]

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

[Minchao Fang @minchaofang]

@KevinKaichuang @WChentong Thanks, Kevin! We’ll be dropping the code and an updated preprint soon—hoping it moves the needle for the field. Would love your take once it’s out.

[Minchao Fang @minchaofang]

As we were about to submit, we were pleased to see parallel work from the Sergey team, which adopted a similar philosophy in exploring
AlphaFold3-like models for protein design. @ChoYehlin @sokrypton
Great to see more research in this space.

https://t.co/sqQGbARin9

[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

[Minchao Fang @minchaofang]

We also used a framework-fixed strategy to design a phospho-specific Aβ targeting antibody, with a binding affinity in the low hundred nM range, specifically binding only to the phosphorylated Aβ.

[Minchao Fang @minchaofang]

We designed seven small molecules or ion binders: ATP, CA, DTG, AD, cAMP, TRP, and Zn2+. For each target, fewer than 16 designs were tested, with at least one binder identified. Five of these binders were further characterized by crystal structures.

[Minchao Fang @minchaofang]

We replace HalluDesign prediction model with protenix, an AF3-style model built on protein language embeddings, which enables successful de novo design of monomers and diverse biomolecular binders by directly initializing random sequences.

[Minchao Fang @minchaofang]

Structure conditioning at different noise level in the structure prediction stage allows precise control over the sampling space, facilitating tasks from local and global protein optimization to de novo design.

[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