18 papers
Is Retrieval All You Need? Assessment and Emergence of Novelty in Protein Structure Generation
Tongyue Xu, Yijie Zhang, Mutian He +4
Protein backbone generation models are often credited with exploring novel fold space based solely on low full-chain similarity to known proteins, yet this cannot distinguish a gen…
Multimodal Regression for Enzyme Turnover Rates Prediction
Bozhen Hu, Cheng Tan, Siyuan Li +4
The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most org…
Protein-SE(3): Benchmarking SE(3)-based Generative Models for Protein Structure Design
Lang Yu, Zhangyang Gao, Cheng Tan +3
SE(3)-based generative models have shown great promise in protein geometry modeling and effective structure design. However, the field currently lacks a modularized benchmark to en…
MogaNet: Multi-order Gated Aggregation Network
Siyuan Li, Zedong Wang, Zicheng Liu +6
By contextualizing the kernel as global as possible, Modern ConvNets have shown great potential in computer vision tasks. However, recent progress on multi-order game-theoretic int…
AlphaFold Database Debiasing for Robust Inverse Folding
Cheng Tan, Zhenxiao Cao, Zhangyang Gao +3
The AlphaFold Protein Structure Database (AFDB) offers unparalleled structural coverage at near-experimental accuracy, positioning it as a valuable resource for data-driven protein…
Mitigating Prior Shape Bias in Point Clouds via Differentiable Center Learning
Zhe Li, Xiying Wang, Jinglin Zhao +3
Masked autoencoding and generative pretraining have achieved remarkable success in computer vision and natural language processing, and more recently, they have been extended to th…