Structure-aware protein-protein interaction site prediction using deep graph convolutional network. - Qianmu Yuan; Jianwen Chen; Huiying Zhao; Yaoqi Zhou; Yuedong Yang (Bioinform., 2021)

AlphaFold2-aware protein-DNA binding site prediction using graph transformer. - Qianmu Yuan; Sheng Chen; Jiahua Rao; Shuangjia Zheng; Huiying Zhao; Yuedong Yang (Briefings Bioinform., 2022)

Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning. - Qianmu Yuan; Sheng Chen; Yu Wang 027; Huiying Zhao; Yuedong Yang (Briefings Bioinform., 2022)

Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model. - Yuansong Zeng; Zhuoyi Wei; Qianmu Yuan; Sheng Chen; Weijiang Yu; Yutong Lu; Jianzhao Gao; Yuedong Yang (Bioinform., 2023)

Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion. - Qianmu Yuan; Junjie Xie; Jiancong Xie; Huiying Zhao; Yuedong Yang (Briefings Bioinform., 2023)

Fast and accurate protein intrinsic disorder prediction by using a pretrained language model. - Yidong Song; Qianmu Yuan; Sheng Chen; Ken Chen 006; Yaoqi Zhou; Yuedong Yang (Briefings Bioinform., 2023)

Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures. - Yidong Song; Qianmu Yuan; Huiying Zhao; Yuedong Yang (Briefings Bioinform., 2023)

DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model. - Yitian Fang; Yi Jiang; Leyi Wei; Qin Ma 003; Zhixiang Ren; Qianmu Yuan; Dong-Qing Wei (Bioinform., 2023)

GP-nano: a geometric graph network for nanobody polyreactivity prediction. - Xiaolong Zhou; Qianmu Yuan; Shuangjia Zheng; Yu Wang 027; Yuedong Yang (BIBM, 2024)

Predicting the effects of mutations on protein solubility using graph convolution network and protein language model representation. - Jing Wang 208; Sheng Chen; Qianmu Yuan; Jianwen Chen; Danping Li; Lei Wang; Yuedong Yang (J. Comput. Chem., 2024)

A 3D pocket-aware and evolutionary conserved interaction guided diffusion model for molecular optimization. - Anjie Qiao; Hao Zhang; Qianmu Yuan; Qirui Deng; Jingtian Su; Weifeng Huang; Huihao Zhou; Guo-Bo Li; Zhen Wang; Jinping Lei (CoRR, 2025)