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q-bio.BM2025★ 1 cited
SeedFold: Scaling Biomolecular Structure Prediction
Yi Zhou, Chan Lu, Yiming Ma +6
Highly accurate biomolecular structure prediction is a key component of developing biomolecular foundation models, and one of the most critical aspects of building foundation model…
q-bio.BM2025★ 1 cited
SeedProteo: Accurate De Novo All-Atom Design of Protein Binders
Wei Qu, Yiming Ma, Fei Ye +6
We present SeedProteo, a diffusion-based model for de novo all-atom protein design. We demonstrate how to repurpose a cutting-edge folding architecture into a powerful generative d…
q-bio.BM2024
ProteinWeaver: A Divide-and-Assembly Approach for Protein Backbone Design
Yiming Ma, Fei Ye, Yi Zhou +3
Nature creates diverse proteins through a 'divide and assembly' strategy. Inspired by this idea, we introduce ProteinWeaver, a two-stage framework for protein backbone design. Our…