Improving the Scoring of Protein-Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization. - Jinfeng Liu 004; Xiao He 004; John Z. H. Zhang (J. Chem. Inf. Model., 2013)

PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity. - Xiao Liu; Jinfeng Liu 004; Tong Zhu; Lujia Zhang; Xiao He 004; John Z. H. Zhang (J. Chem. Inf. Model., 2016)

A Semiautomated Structure-Based Method To Predict Substrates of Enzymes via Molecular Docking: A Case Study with Candida antarctica Lipase B. - Zhiqiang Yao; Lujia Zhang; Bei Gao; Dongbing Cui; Fengqing Wang; Xiao He 004; John Z. H. Zhang; Dongzhi Wei (J. Chem. Inf. Model., 2016)

Fragment-based quantum mechanical calculation of protein-protein binding affinities. - Yaqian Wang; Jinfeng Liu 004; Jinjin Li; Xiao He 004 (J. Comput. Chem., 2018)

Development of a New Scoring Function for Virtual Screening: APBScore. - Jingxiao Bao; Xiao He 004; John Z. H. Zhang (J. Chem. Inf. Model., 2020)

DeepBSP - a Machine Learning Method for Accurate Prediction of Protein-Ligand Docking Structures. - Jingxiao Bao; Xiao He 004; John Z. H. Zhang (J. Chem. Inf. Model., 2021)

Discovering inhibitors of TEAD palmitate binding pocket through virtual screening and molecular dynamics simulation. - Yimin Li; Yaqi Li; Chao Ning 009; Jianda Yue; Cheng Zhang; Xiao He 004; Ying Wang 069; Zhonghua Liu (Comput. Biol. Chem., 2022)

Discovery of Mcl-1 inhibitors through virtual screening, molecular dynamics simulations and in vitro experiments. - Jianda Yue; Yaqi Li; Fengjiao Li; Peng Zhang; Yimin Li; Jiawei Xu; Qianqian Zhang; Cheng Zhang; Xiao He 004; Ying Wang 069; Zhonghua Liu (Comput. Biol. Medicine, 2023)

Evolutionary Retrosynthetic Route Planning. - Yan Zhang 116; Hao Hao; Xiao He 004; Shuanhu Gao; Aimin Zhou (CoRR, 2023)

Supervised learning of a chemistry functional with damped dispersion. - Yiwei Liu; Cheng Zhang; Zhonghua Liu; Donald G. Truhlar; Ying Wang 069; Xiao He 004 (Nat. Comput. Sci., 2023)

Deep Learning with Geometry-Enhanced Molecular Representation for Augmentation of Large-Scale Docking-Based Virtual Screening. - Lan Yu; Xiao He 004; Xiaomin Fang; Lihang Liu; Jinfeng Liu 004 (J. Chem. Inf. Model., 2023)

Pushing the Limit of Quantum Mechanical Simulation to the Raman Spectra of a Biological System with 100 Million Atoms. - Honghui Shang; Ying Liu 055; Zhikun Wu; Zhenchuan Chen; Jinfeng Liu 004; Meiyue Shao; Yingzhou Li; Bowen Kan; Huimin Cui; Xiaobing Feng 002; Yunquan Zhang; Donald G. Truhlar; et al. (SC, 2024)

Zeoformer: Coarse-Grained Periodic Graph Transformer for OSDA-Zeolite Affinity Prediction. - Xiangxiang Shen; Zheng Wan; Lingfeng Wen; Licheng Sun; Ou Yang Ming Jie; Xuan Tang; Xian Zeng; Mingsong Chen 001; Xiao He 004; Xian Wei (CoRR, 2024)

Graph Curvature Flow-Based Masked Attention. - Yili Chen; Zheng Wan; Yangyang Li; Xiao He 004; Xian Wei; Jun Han (J. Chem. Inf. Model., 2024)

Evolutionary Retrosynthetic Route Planning [Research Frontier]. - Yan Zhang 116; Xiao He 004; Shuanhu Gao; Aimin Zhou; Hao Hao (IEEE Comput. Intell. Mag., 2024)

Teaching spin symmetry while learning neural network wave functions. - Yongle Li; Yuhao Chen; Xiao He 004 (Nat. Comput. Sci., 2024)

A Hyperbolic Discrete Diffusion 3D RNA Inverse Folding Model for Functional RNA Design. - Dongyue Hou; Shuai Zhang; Mengyao Ma; Hanbo Lin; Zheng Wan; Hui Zhao; Ruian Zhou; Xiao He 004; Xian Wei; Dianwen Ju; Xian Zeng (J. Chem. Inf. Model., 2025)

Transfer Learning for Predicting ncRNA-Protein Interactions. - Yuao Zeng; Lamei Liu; Danyang Xiong; Zheng Wan; Zedong Bi; Xian Zeng; Xian Wei; Xiao He 004 (J. Chem. Inf. Model., 2025)

RetroEA: An efficient evolutionary algorithm for retrosynthetic route planning. - Yan Zhang 116; Hao Hao; Xiao He 004; Aimin Zhou (Swarm Evol. Comput., 2025)