Exhaustively Exploring the Prevalent Interaction Pathways of Ligands Targeting the Ligand-Binding Pocket of Farnesoid X Receptor via Combined Enhanced Sampling. - Sutong Xiang; Zhe Wang 041; Rongfan Tang; Lingling Wang; Qinghua Wang; Yang Yu; Qirui Deng; Tingjun Hou; Haiping Hao; Huiyong Sun (J. Chem. Inf. Model., 2023)

RLpMIEC: High-Affinity Peptide Generation Targeting Major Histocompatibility Complex-I Guided and Interpreted by Interaction Spectrum-Navigated Reinforcement Learning. - Qirui Deng; Zhe Wang 041; Sutong Xiang; Qinghua Wang; Yifei Liu; Tingjun Hou; Huiyong Sun (J. Chem. Inf. Model., 2024)

Characterizing the Cooperative Effect of PROTAC Systems with End-Point Binding Free Energy Calculation. - Kexin Xu; Zhe Wang 041; Sutong Xiang; Rongfan Tang; Qirui Deng; Jingxuan Ge; Zhiliang Jiang; Kaimo Yang; Tingjun Hou; Huiyong Sun (J. Chem. Inf. Model., 2024)

A 3D pocket-aware lead optimization model with knowledge guidance and its application for discovery of new glutaminyl cyclase inhibitors. - Anjie Qiao; Yuting Chen; Junjie Xie; Weifeng Huang; Hao Zhang; Qirui Deng; Jiahua Rao; Ji Deng; Fanbo Meng; Zhen Wang 004; Mingyuan Xu; Hongming Chen 001; et al. (Briefings Bioinform., 2025)

A Unified Deep Graph Model for Identifying the Molecular Categories of Ligands Targeting Nuclear Receptors. - Kaimo Yang; Dejun Jiang 002; Qirui Deng; Sutong Xiang; Jingxuan Ge; Kexin Xu; Zhiliang Jiang; Zihao Wang; Chen Yin; Youqiao Qian; Tingjun Hou; Huiyong Sun (J. Chem. Inf. Model., 2025)

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)