3 papers
q-bio.QM2026
ProtDBench: A Unified Benchmark of Protein Binder Design and Evaluation
Cong Liu, Milong Ren, Jiaqi Guan +4
Recent advances in de novo protein binder design have enabled increasing experimental validation, yet reported in silico metrics remain difficult to interpret or compare across stu…
q-bio.QM2026
A-CODE: Fully Atomic Protein Co-Design with Unified Multimodal Diffusion
Chaoran Cheng, Jiaqi Guan, Milong Ren +5
We present A-CODE, a fully atomic unified one-stage protein co-design model that simultaneously refines discrete atom types and continuous atom coordinates. Unlike predominant two-…
cs.LG2024
Improving Molecular Graph Generation with Flow Matching and Optimal Transport
Xiaoyang Hou, Tian Zhu, Milong Ren +4
Generating molecular graphs is crucial in drug design and discovery but remains challenging due to the complex interdependencies between nodes and edges. While diffusion models hav…