4 papers
Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design
Chen Wei, Fanding Xu, Minghao Sun +5
Proteins perform their biological functions through three-dimensional structures encoded by amino acid sequences, and ligand-binding protein co-design requires models that generate…
EnzyControl: Adding Functional and Substrate-Specific Control for Enzyme Backbone Generation
Chao Song, Zhiyuan Liu, Han Huang +6
Designing enzyme backbones with substrate-specific functionality is a critical challenge in computational protein engineering. Current generative models excel in protein design but…
Learning 3D Anisotropic Noise Distributions Improves Molecular Force Field Modeling
Xixian Liu, Rui Jiao, Zhiyuan Liu +6
Coordinate denoising has emerged as a promising method for 3D molecular pretraining due to its theoretical connection to learning molecular force field. However, existing denoising…
PRING: Rethinking Protein-Protein Interaction Prediction from Pairs to Graphs
Xinzhe Zheng, Hao Du, Fanding Xu +9
Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on iso…