Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning? - Shukai Gu; Chao Shen 008; Jiahui Yu; Hong Zhao; Huanxiang Liu; Liwei Liu; Rong Sheng; Lei Xu 035; Zhe Wang 041; Tingjun Hou; Yu Kang 002 (Briefings Bioinform., 2023)

In-depth theoretical modeling to explore the mechanism of TPX-0131 overcoming lorlatinib resistance to ALKL1196M/G1202R mutation. - Xing Zhang; Jianbo Tong; Tianhao Wang; Zhe Wang 041; Shukai Gu; Lei Xu 035; Tingjun Hou; Peichen Pan (Comput. Biol. Medicine, 2024)

Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios. - Shukai Gu; Yuwei Yang; Yihao Zhao; Jiayue Qiu; Xiaorui Wang; Henry Hoi Yee Tong; Liwei Liu; Xiaozhe Wan; Huanxiang Liu; Tingjun Hou; Yu Kang 002 (J. Chem. Inf. Model., 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)