Ligand Identification Scoring Algorithm (LISA). - Zheng Zheng 002; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2011)

Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores. - Mark L. Benson; John C. Faver; Melek N. Ucisik; Danial S. Dashti; Zheng Zheng 002; Kenneth M. Merz Jr. (J. Comput. Aided Mol. Des., 2012)

Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein-Ligand Interactions. - Zheng Zheng 002; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2013)

On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge. - Nupur Bansal; Zheng Zheng 002; David S. Cerutti; Kenneth M. Merz Jr. (J. Comput. Aided Mol. Des., 2017)

Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge. - Lin Frank Song; Nupur Bansal; Zheng Zheng 002; Kenneth M. Merz Jr. (J. Comput. Aided Mol. Des., 2018)

Random Forest Refinement of Pairwise Potentials for Protein-Ligand Decoy Detection. - Jun Pei; Zheng Zheng 002; Hyunji Kim; Lin Frank Song; Sarah Walworth; Margaux R. Merz; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2019)

Random Forest Refinement of the KECSA2 Knowledge-Based Scoring Function for Protein Decoy Detection. - Jun Pei; Zheng Zheng 002; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2019)

MovableType Software for Fast Free Energy-Based Virtual Screening: Protocol Development, Deployment, Validation, and Assessment. - Zheng Zheng 002; Oleg Y. Borbulevych; Hao Liu; Jianpeng Deng; Roger I. Martin; Lance M. Westerhoff (J. Chem. Inf. Model., 2020)

The Conformational Transition Pathways and Hidden Intermediates in DFG-Flip Process of c-Met Kinase Revealed by Metadynamics Simulations. - Tao Jiang; Zhenhao Liu; Wenlang Liu; Jiawen Chen; Zheng Zheng 002; Mojie Duan (J. Chem. Inf. Model., 2022)

Free Energy Calculations Using the Movable Type Method with Molecular Dynamics Driven Protein-Ligand Sampling. - Wenlang Liu; Zhenhao Liu; Hao Liu; Lance M. Westerhoff; Zheng Zheng 002 (J. Chem. Inf. Model., 2022)

Molecular Insights on the Conformational Transitions and Activity Regulation of the c-Met Kinase Induced by Ligand Binding. - Zhenhao Liu; Kuan Liang; Wenlang Liu; Tao Jiang; Rui Zhou; Mojie Duan; Zheng Zheng 002 (J. Chem. Inf. Model., 2023)

DihedralsDiff: A Diffusion Conformation Generation Model That Unifies Local and Global Molecular Structures. - Jianhui Xiao; Zheng Zheng 002; Hao Liu (J. Chem. Inf. Model., 2025)

Accommodating Statistical and Physics-Based Computational Protocols for Molecular Glue Model and Evaluation. - Qixuan Xu; Wenlang Liu; Hao Liu; Zheng Zheng 002 (J. Chem. Inf. Model., 2025)