Efficient Computational Framework for Target-Specific Active Peptide Discovery: A Case Study on IL-17C Targeting Cyclic Peptides. - Zhipeng Wu; Yejian Wu; Cheng Zhu; Xinyi Wu; Silong Zhai; Xinqiao Wang; Zhihao Su; Hongliang Duan (J. Chem. Inf. Model., 2023)

GAPS: a geometric attention-based network for peptide binding site identification by the transfer learning approach. - Cheng Zhu; Chengyun Zhang; Tianfeng Shang; Chenhao Zhang; Silong Zhai; Lujing Cao; Zhenyu Xu; Zhihao Su; Ying Song; An Su; Chengxi Li 002; Hongliang Duan (Briefings Bioinform., 2024)

PepPCBench is a Comprehensive Benchmarking Framework for Protein-Peptide Complex Structure Prediction. - Silong Zhai; Huifeng Zhao; Jike Wang; Shaolong Lin; Tiantao Liu; Shukai Gu; Dejun Jiang 002; Huanxiang Liu; Yu Kang 002; Xiaojun Yao; Tingjun Hou (J. Chem. Inf. Model., 2025)

Benchmarking AI-powered docking methods from the perspective of virtual screening. - Shukai Gu; Chao Shen 008; Xujun Zhang; Huiyong Sun; Heng Cai; Hao Luo; Huifeng Zhao; Bo Liu; Hongyan Du; Yihao Zhao; Chenggong Fu; Silong Zhai; et al. (Nat. Mac. Intell., 2025)