Author

Yan Chen

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#machine learning Open access May 2025

EpiMII: Integrating Structure and Graph Neural Networks for MHC-II Epitope and Neoantigen Design

EpiMII is presented, a Graph Neural Network model for MHC-II epitope design, which learns from the structural features of epitopes to predict their sequences, potentially contributing to vaccine development.

Jiayi Yuan, Xiaowei Xu, Ze-Yu Sun et al. · bioRxiv · 1 citation

#machine learning Open access Jun 2025

AntiBMPNN: Structure‐Guided Graph Neural Networks for Precision Antibody Engineering

AntiBMPNN consistently outperforms AbMPNN, AntiFold, and ProteinMPNN in designing complementarity determining regions (CDR) 1‐3, yielding stronger binding affinities and confirming its potential to improve therapeutic antibody design.

Ze-Yu Sun, Jiayi Yuan, Divya Jaiswal et al. · Advancement of science · 9 citations