EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling. - Qianzhen Shao; Yaoyukun Jiang; Zhongyue J. Yang (J. Chem. Inf. Model., 2022)

IntEnzyDB: an Integrated Structure-Kinetics Enzymology Database. - Bailu Yan; Xinchun Ran; Anvita Gollu; Zihao Cheng; Xiang Zhou; Yiwen Chen; Zhongyue J. Yang (J. Chem. Inf. Model., 2022)

LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling. - Reecan J. Juarez; Yaoyukun Jiang; Matthew Tremblay; Qianzhen Shao; A. James Link; Zhongyue J. Yang (J. Chem. Inf. Model., 2023)

EnzyHTP Computational Directed Evolution with Adaptive Resource Allocation. - Qianzhen Shao; Yaoyukun Jiang; Zhongyue J. Yang (J. Chem. Inf. Model., 2023)

Physics-based modeling in the new era of enzyme engineering. - Christopher P. Jurich; Qianzhen Shao; Xinchun Ran; Zhongyue J. Yang (Nat. Comput. Sci., 2025)