Computation of Octanol-Water Partition Coefficients by Guiding an Additive Model with Knowledge. - Tiejun Cheng; Yuan Zhao; Xun Li; Fu Lin; Yong Xu; Xing-long Zhang; Yan Li 051; Renxiao Wang; Luhua Lai (J. Chem. Inf. Model., 2007)

Comparative Assessment of Scoring Functions on a Diverse Test Set. - Tiejun Cheng; Xun Li; Yan Li 051; Zhihai Liu; Renxiao Wang (J. Chem. Inf. Model., 2009)

Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes. - Xun Li; Yan Li 051; Tiejun Cheng; Zhihai Liu; Renxiao Wang (J. Comput. Chem., 2010)

Test MM-PB/SA on True Conformational Ensembles of Protein-Ligand Complexes. - Yan Li 051; Zhihai Liu; Renxiao Wang (J. Chem. Inf. Model., 2010)

Automatic Tailoring and Transplanting: A Practical Method that Makes Virtual Screening More Useful. - Yan Li 051; Yuan Zhao; Zhihai Liu; Renxiao Wang (J. Chem. Inf. Model., 2011)

Mining the Characteristic Interaction Patterns on Protein-Protein Binding Interfaces. - Yan Li 051; Zhihai Liu; Li Han; Chengke Li; Renxiao Wang (J. Chem. Inf. Model., 2013)

Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results. - Yan Li 051; Li Han; Zhihai Liu; Renxiao Wang (J. Chem. Inf. Model., 2014)

Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set. - Yan Li 051; Zhihai Liu; Jie Li; Li Han; Jie Liu; Zhixiong Zhao; Renxiao Wang (J. Chem. Inf. Model., 2014)

PDB-wide collection of binding data: current status of the PDBbind database. - Zhihai Liu; Yan Li 051; Li Han; Jie Li; Jie Liu; Zhixiong Zhao; Wei Nie; Yuchen Liu; Renxiao Wang (Bioinform., 2015)

AutoT&T v.2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization. - Yan Li 051; Zhixiong Zhao; Zhihai Liu; Minyi Su; Renxiao Wang (J. Chem. Inf. Model., 2016)

Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints. - Jie Liu; Minyi Su; Zhihai Liu; Jie Li; Yan Li 051; Renxiao Wang (BMC Bioinform., 2017)

Comparative Assessment of Scoring Functions: The CASF-2016 Update. - Minyi Su; Qifan Yang; Yu Du; Guoqin Feng; Zhihai Liu; Yan Li 051; Renxiao Wang (J. Chem. Inf. Model., 2019)

Revisiting the Relationship Between Correlation Coefficient, Confidence Level, and Sample Size. - Qifan Yang; Minyi Su; Yan Li 051; Renxiao Wang (J. Chem. Inf. Model., 2019)

Prediction of the Favorable Hydration Sites in a Protein Binding Pocket and Its Application to Scoring Function Formulation. - Yan Li 051; Yingduo Gao; M. Katharine Holloway; Renxiao Wang (J. Chem. Inf. Model., 2020)

Fragment-Based Computational Method for Designing GPCR Ligands. - Yan Li 051; Yaping Sun; Yunpeng Song; Dongcheng Dai; Zhixiong Zhao; Qing Zhang; Wenge Zhong; Liaoyuan A. Hu; Yingli Ma; Xun Li; Renxiao Wang (J. Chem. Inf. Model., 2020)

Tapping on the Black Box: How Is the Scoring Power of a Machine-Learning Scoring Function Dependent on the Training Set? - Minyi Su; Guoqin Feng; Zhihai Liu; Yan Li 051; Renxiao Wang (J. Chem. Inf. Model., 2020)

Analysis of the Binding Sites on BAX and the Mechanism of BAX Activators through Extensive Molecular Dynamics Simulations. - Guoqin Feng; Xiangying Zhang; Yan Li 051; Renxiao Wang (J. Chem. Inf. Model., 2022)

HydraMap v.2: Prediction of Hydration Sites and Desolvation Energy with Refined Statistical Potentials. - Yan Li 051; Zhe Zhang; Renxiao Wang (J. Chem. Inf. Model., 2023)

COMET:Combined Matrix for Elucidating Targets. - Haojie Wang; Zhe Zhang; Haotian Gao; Xiangying Zhang; Jingyuan Li; Zhihang Chen; Xinchong Chen; Yifei Qi; Yan Li 051; Renxiao Wang (CoRR, 2024)

PLANET: A Multi-objective Graph Neural Network Model for Protein-Ligand Binding Affinity Prediction. - Xiangying Zhang; Haotian Gao; Haojie Wang; Zhihang Chen; Zhe Zhang; Xinchong Chen; Yan Li 051; Yifei Qi; Renxiao Wang (J. Chem. Inf. Model., 2024)

Computational Methods for Predicting Chemical Reactivity of Covalent Compounds. - Zhe Zhang; Ruyu Gao; Meiling Zhao; Xiangying Zhang; Haotian Gao; Yifei Qi; Renxiao Wang; Yan Li 051 (J. Chem. Inf. Model., 2025)