Generalized Born Based Continuous Constant pH Molecular Dynamics in Amber: Implementation, Benchmarking and Analysis. - Yandong Huang; Robert C. Harris; Jana Shen (J. Chem. Inf. Model., 2018)

Basis for Accurate Protein pKa Prediction with Machine Learning. - Zhitao Cai; Tengzi Liu; Qiaoling Lin; Jiahao He; Xiaowei Lei; Fangfang Luo; Yandong Huang (J. Chem. Inf. Model., 2023)

DeepKa Web Server: High-Throughput Protein pKa Prediction. - Zhitao Cai; Hao Peng; Shuo Sun; Jiahao He; Fangfang Luo; Yandong Huang (J. Chem. Inf. Model., 2024)