New approach for representation of molecular surface. - Wensheng Cai; Maosen Zhang; Bernard Maigret (J. Comput. Chem., 1998)

A fast annealing evolutionary algorithm for global optimization. - Wensheng Cai; Xueguang Shao (J. Comput. Chem., 2002)

Global Optimization of Lennard-Jones Clusters by a Parallel Fast Annealing Evolutionary Algorithm. - Wensheng Cai; Haiyan Jiang; Xueguang Shao (J. Chem. Inf. Comput. Sci., 2002)

A dynamic lattice searching method for fast optimization of Lennard-Jones clusters. - Xueguang Shao; Longjiu Cheng; Wensheng Cai (J. Comput. Chem., 2004)

Parallel Random Tunneling Algorithm for Structural Optimization of Lennard-Jones Clusters up to N = 330. - Xueguang Shao; Haiyan Jiang; Wensheng Cai (J. Chem. Inf. Model., 2004)

Consensus analysis of multiple classifiers using non-repetitive variables: Diagnostic application to microarray gene expression data. - Zhenqiang Su; Huixiao Hong; Roger Perkins; Xueguang Shao; Wensheng Cai; Weida Tong (Comput. Biol. Chem., 2007)

A dynamic lattice searching method with constructed core for optimization of large lennard-jones clusters. - Xiaoli Yang; Wensheng Cai; Xueguang Shao (J. Comput. Chem., 2007)

A dynamic lattice searching method with interior operation for unbiased optimization of large Lennard-Jones clusters. - Xueguang Shao; Xiaoli Yang; Wensheng Cai (J. Comput. Chem., 2008)

Optimization of bimetallic Cu-Au and Ag-Au clusters by using a modified adaptive immune optimization algorithm. - Xia Wu; Wensheng Cai; Xueguang Shao (J. Comput. Chem., 2009)

Impact of different potentials on the structures and energies of clusters. - Zhinan Ma; Wensheng Cai; Xueguang Shao (J. Comput. Chem., 2011)

Selecting significant genes by randomization test for cancer classification using gene expression data. - Zhiyi Mao; Wensheng Cai; Xueguang Shao (J. Biomed. Informatics, 2013)

ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines. - Haochuan Chen; Haohao Fu; Xueguang Shao; Christophe Chipot; Wensheng Cai (J. Chem. Inf. Model., 2018)

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations. - Haohao Fu; James C. Gumbart; Haochuan Chen; Xueguang Shao; Wensheng Cai; Christophe Chipot (J. Chem. Inf. Model., 2018)

Changes in Microenvironment Modulate the B- to A-DNA Transition. - Hong Zhang 053; Haohao Fu; Xueguang Shao; François Dehez; Christophe Chipot; Wensheng Cai (J. Chem. Inf. Model., 2019)

Modulation of membrane permeability by carbon dioxide. - Hong Zhang 053; Xueguang Shao; François Dehez; Wensheng Cai; Christophe Chipot (J. Comput. Chem., 2020)

Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD. - Haochuan Chen; Julio D. C. Maia; Brian K. Radak; David J. Hardy; Wensheng Cai; Christophe Chipot; Emad Tajkhorshid (J. Chem. Inf. Model., 2020)

Finding an Optimal Pathway on a Multidimensional Free-Energy Landscape. - Haohao Fu; Haochuan Chen; Xin'ao Wang; Hao Chai; Xueguang Shao; Wensheng Cai; Christophe Chipot (J. Chem. Inf. Model., 2020)

BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations. - Haohao Fu; Haochuan Chen; Wensheng Cai; Xueguang Shao; Christophe Chipot (J. Chem. Inf. Model., 2021)

MLCV: Bridging Machine-Learning-Based Dimensionality Reduction and Free-Energy Calculation. - Haochuan Chen; Han Liu; Heying Feng; Haohao Fu; Wensheng Cai; Xueguang Shao; Christophe Chipot (J. Chem. Inf. Model., 2022)

Hyperactive Antifreeze Proteins Promote Ice Growth before Binding to It. - Shaoli Cui; Weijia Zhang; Xueguang Shao; Wensheng Cai (J. Chem. Inf. Model., 2022)

Spectral Encoder to Extract the Features of Near-Infrared Spectra for Multivariate Calibration. - Chaoshu Duan; Xuyang Liu; Wensheng Cai; Xueguang Shao (J. Chem. Inf. Model., 2022)

Accurate Description of Solvent-Exposed Salt Bridges with a Non-polarizable Force Field Incorporating Solvent Effects. - Han Liu; Haohao Fu; Christophe Chipot; Xueguang Shao; Wensheng Cai (J. Chem. Inf. Model., 2022)

Binding Models of Aβ42 Peptide with Membranes Explored by Molecular Simulations. - Ke Wang; Xueguang Shao; Wensheng Cai (J. Chem. Inf. Model., 2022)

Achieving Accurate Standard Protein-Protein Binding Free Energy Calculations through the Geometrical Route and Ergodic Sampling. - Haohao Fu; Christophe Chipot; Xueguang Shao; Wensheng Cai (J. Chem. Inf. Model., 2023)

Binding Thermodynamics of Fourth-Generation EGFR Inhibitors Revealed by Absolute Binding Free Energy Calculations. - Huaxin Zhou; Haohao Fu; Xueguang Shao; Wensheng Cai (J. Chem. Inf. Model., 2023)

PGAT-ABPp: harnessing protein language models and graph attention networks for antibacterial peptide identification with remarkable accuracy. - Yuelei Hao; Xuyang Liu; Haohao Fu; Xueguang Shao; Wensheng Cai (Bioinform., 2024)

Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C-H Acids. - Hongle An; Xuyang Liu; Wensheng Cai; Xueguang Shao (J. Chem. Inf. Model., 2024)

AttenGpKa: A Universal Predictor of Solvation Acidity Using Graph Neural Network and Molecular Topology. - Hongle An; Xuyang Liu; Wensheng Cai; Xueguang Shao (J. Chem. Inf. Model., 2024)

Interpretable Perturbator for Variable Selection in near-Infrared Spectral Analysis. - Chaoshu Duan; Xuyang Liu; Wensheng Cai; Xueguang Shao (J. Chem. Inf. Model., 2024)

SpeLL: An Agent for Natural Language-Driven Intelligent Spectral Modeling. - Jiashun Fu; Xuyang Liu; Wensheng Cai; Haohao Fu; Xueguang Shao (J. Chem. Inf. Model., 2025)

Accurate Prediction of CRISPR/Cas13a Guide Activity Using Feature Selection and Deep Learning. - Jiashun Fu; Xuyang Liu; Ruijie Deng; Xiue Jiang; Wensheng Cai; Haohao Fu; Xueguang Shao (J. Chem. Inf. Model., 2025)

Head-to-Tail Cyclization Enhances Ice-Growth Inhibition by Linear Threonine Oligomers. - Haipeng Wang; Xuyang Liu; Wensheng Cai; Xueguang Shao (J. Chem. Inf. Model., 2025)