DRlinker: Deep Reinforcement Learning for Optimization in Fragment Linking Design. - Youhai Tan; Lingxue Dai; Weifeng Huang; Yinfeng Guo; Shuangjia Zheng; Jinping Lei; Hongming Chen 001; Yuedong Yang (J. Chem. Inf. Model., 2022)

How Good are Current Pocket-Based 3D Generative Models?: The Benchmark Set and Evaluation of Protein Pocket-Based 3D Molecular Generative Models. - Haoyang Liu; Yifei Qin; Zhangming Niu; Mingyuan Xu; Jiaqiang Wu; Xianglu Xiao; Jinping Lei; Ting Ran; Hongming Chen 001 (J. Chem. Inf. Model., 2024)

DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model. - Junjie Xie; Sheng Chen; Jinping Lei; Yuedong Yang (J. Chem. Inf. Model., 2024)

GRELinker: A Graph-Based Generative Model for Molecular Linker Design with Reinforcement and Curriculum Learning. - Hao Zhang; Jinchao Huang 004; Junjie Xie; Weifeng Huang; Yuedong Yang; Mingyuan Xu; Jinping Lei; Hongming Chen 001 (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)

Systematic Parameter Decision in Approximate Model Counting. - Jinping Lei; Toru Takisaka; Junqiang Peng 001; Mingyu Xiao 001 (CoRR, 2025)

A 3D pocket-aware and affinity-guided diffusion model for lead optimization. - Anjie Qiao; Junjie Xie; Weifeng Huang; Hao Zhang; Jiahua Rao; Shuangjia Zheng; Yuedong Yang; Zhen Wang 036; Guo-Bo Li; Jinping Lei (CoRR, 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)