Design of AI-Enhanced Drug Lead Optimization Workflow for HPC and Cloud. - Chih-Chieh Yang; Giacomo Domeniconi; Leili Zhang; Guojing Cong (IEEE BigData, 2020)

CASTELO: clustered atom subtypes aided lead optimization - a combined machine learning and molecular modeling method. - Leili Zhang; Giacomo Domeniconi; Chih-Chieh Yang; Seung-gu Kang; Ruhong Zhou; Guojing Cong (BMC Bioinform., 2021)

In-Pocket 3D Graphs Enhance Ligand-Target Compatibility in Generative Small-Molecule Creation. - Seung-gu Kang; Jeffrey K. Weber; Joseph A. Morrone; Leili Zhang; Tien Huynh; Wendy D. Cornell (CoRR, 2022)

Simplified, interpretable graph convolutional neural networks for small molecule activity prediction. - Jeffrey K. Weber; Joseph A. Morrone; Sugato Bagchi; Jan D. Estrada Pabon; Seung-gu Kang; Leili Zhang; Wendy D. Cornell (J. Comput. Aided Mol. Des., 2022)

Research on Uncertainty of Landslide Susceptibility Prediction - Bibliometrics and Knowledge Graph Analysis. - Zhengli Yang; Chao Liu 030; Ruihua Nie; Wanchang Zhang 001; Leili Zhang; Zhijie Zhang 002; Weile Li; Gang Liu 005; Xiaoai Dai; Donghui Zhang; Min Zhang; Shuangxi Miao; et al. (Remote. Sens., 2022)

Scalable multiscale modeling of platelets with 100 million particles. - Changnian Han; Peng Zhang; Yicong Zhu; Guojing Cong; James R. Kozloski; Chih-Chieh Yang; Leili Zhang; Yuefan Deng (J. Supercomput., 2022)

AI-aided multiscale modeling of physiologically-significant blood clots. - Yicong Zhu; Changnian Han; Peng Zhang; Guojing Cong; James R. Kozloski; Chih-Chieh Yang; Leili Zhang; Yuefan Deng (Comput. Phys. Commun., 2023)

Unsupervised and supervised AI on molecular dynamics simulations reveals complex characteristics of HLA-A2-peptide immunogenicity. - Jeffrey K. Weber; Joseph A. Morrone; Seung-gu Kang; Leili Zhang; Lijun Lang; Diego Chowell; Chirag Krishna; Tien Huynh; Prerana Parthasarathy; Binquan Luan; Tyler J. Alban; Wendy D. Cornell; et al. (Briefings Bioinform., 2024)

Learning coarse-grained force fields for fibrogenesis modeling. - Ziji Zhang; Georgios Kementzidis; Peng Zhang 006; Leili Zhang; James R. Kozloski; Adam Hansen; Miriam Rafailovich; Marcia Simon; Yuefan Deng (Comput. Phys. Commun., 2024)

Integrating Physics-Based Simulations with Data-Driven Deep Learning Represents a Robust Strategy for Developing Inhibitors Targeting the Main Protease. - Yanqing Yang; Yangwei Jiang; Dong Zhang; Leili Zhang; Ruhong Zhou (J. Chem. Inf. Model., 2025)