Improved fragment sampling for ab initio protein structure prediction using deep neural networks. - Tong Wang 014; Yanhua Qiao; Wenze Ding; Wenzhi Mao; Yaoqi Zhou; Haipeng Gong (Nat. Mach. Intell., 2019)

AmoebaContact and GDFold as a pipeline for rapid de novo protein structure prediction. - Wenzhi Mao; Wenze Ding; Yaoguang Xing; Haipeng Gong (Nat. Mach. Intell., 2020)

SAMF: a self-adaptive protein modeling framework. - Wenze Ding; Qijiang Xu; Siyuan Liu 005; Tong Wang 014; Bin Shao; Haipeng Gong; Tie-Yan Liu (Bioinform., 2021)

Protein design via deep learning. - Wenze Ding; Kenta Nakai; Haipeng Gong (Briefings Bioinform., 2022)

IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits. - Daniel Mechtersheimer; Wenze Ding; Xiangnan Xu; Sanghyun Kim; Carolyn Sue; Yue Cao; Jean Y. H. Yang (Bioinform., 2025)