Protein ligand docking based on empirical method for binding affinity estimation. - Peng Tao 001; Luhua Lai (J. Comput. Aided Mol. Des., 2001)

A toolkit to assist ONIOM calculations. - Peng Tao 001; H. Bernhard Schlegel (J. Comput. Chem., 2010)

Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery. - Robert Kalescky; Hongyu Zhou; Jin Liu 005; Peng Tao 001 (PLoS Comput. Biol., 2016)

Recognition of protein allosteric states and residues: Machine learning approaches. - Hongyu Zhou; Zheng Dong; Peng Tao 001 (J. Comput. Chem., 2018)

An Orbital-Overlap Complement to Ligand and Binding Site Electrostatic Potential Maps. - Arshad Mehmood; Stephanie I. Jones; Peng Tao 001; Benjamin G. Janesko (J. Chem. Inf. Model., 2018)

Dynamical Behavior of β-Lactamases and Penicillin- Binding Proteins in Different Functional States and Its Potential Role in Evolution. - Feng Wang 068; Hongyu Zhou; Xinlei Wang 001; Peng Tao 001 (Entropy, 2019)

Probing Protein Allostery as a Residue-Specific Concept via Residue Response Maps. - Hamed S. Hayatshahi; Emilio Ahuactzin; Peng Tao 001; Shouyi Wang; Jin Liu 005 (J. Chem. Inf. Model., 2019)

Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis. - Hongyu Zhou; Zheng Dong; Gennady Verkhivker; Brian D. Zoltowski; Peng Tao 001 (PLoS Comput. Biol., 2019)

ivis Dimensionality Reduction Framework for Biomacromolecular Simulations. - Hao Tian 010; Peng Tao 001 (J. Chem. Inf. Model., 2020)

PASSer: prediction of allosteric sites server. - Hao Tian 010; Xi Jiang 008; Peng Tao 001 (Mach. Learn. Sci. Technol., 2021)

Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE. - Francesco Trozzi; Feng Wang 068; Gennady Verkhivker; Brian D. Zoltowski; Peng Tao 001 (PLoS Comput. Biol., 2021)

Accurate ADMET Prediction with XGBoost. - Hao Tian; Rajas Ketkar; Peng Tao 001 (CoRR, 2022)

Sparse group selection and analysis of function-related residue for protein-state recognition. - Fangyun Bai; Kin Ming Puk; Jin Liu 005; Hongyu Zhou; Peng Tao 001; Wenyong Zhou; Shouyi Wang (J. Comput. Chem., 2022)

PASSerRank: Prediction of allosteric sites with learning to rank. - Hao Tian 010; Sian Xiao; Xi Jiang 008; Peng Tao 001 (J. Comput. Chem., 2023)

LAST: Latent Space-Assisted Adaptive Sampling for Protein Trajectories. - Hao Tian 010; Xi Jiang 008; Sian Xiao; Hunter La Force; Eric C. Larson; Peng Tao 001 (J. Chem. Inf. Model., 2023)

Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. - Steve Agajanian; Mohammed Alshahrani; Fang Bai; Peng Tao 001; Gennady M. Verkhivker (J. Chem. Inf. Model., 2023)

PASSer: fast and accurate prediction of protein allosteric sites. - Hao Tian 010; Sian Xiao; Xi Jiang 008; Peng Tao 001 (Nucleic Acids Res., 2023)

Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. - Sian Xiao; Mohammed Alshahrani; Grace Gupta; Peng Tao 001; Gennady Verkhivker (J. Chem. Inf. Model., 2023)

AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape. - Nishank Raisinghani; Mohammed Alshahrani; Grace Gupta; Sian Xiao; Peng Tao 001; Gennady Verkhivker (J. Chem. Inf. Model., 2024)

β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. - Sian Xiao; Mayar Tarek Ibrahim; Gennady M. Verkhivker; Brian D. Zoltowski; Peng Tao 001 (J. Comput. Chem., 2024)