| PASSer2.0: accurate prediction of protein allosteric sites through automated machine learning S Xiao, H Tian, P Tao Frontiers in Molecular Biosciences 9, 879251, 2022 | 37 | 2022 |
| PASSer: fast and accurate prediction of protein allosteric sites H Tian, S Xiao, X Jiang, P Tao Nucleic Acids Research 51 (W1), W427–W431, 2023 | 36 | 2023 |
| Explore protein conformational space with variational autoencoder H Tian, X Jiang, F Trozzi, S Xiao, EC Larson, P Tao Frontiers in Molecular Biosciences 8, 781635, 2021 | 35 | 2021 |
| PASSerRank: prediction of allosteric sites with learning to rank H Tian, S Xiao, X Jiang, P Tao Journal of Computational Chemistry 44 (28), 2223-2229, 2023 | 18 | 2023 |
| Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variants … S Xiao, M Alshahrani, G Gupta, P Tao, G Verkhivker Journal of Chemical Information and Modeling 63 (16), 5272-5296, 2023 | 18 | 2023 |
| Machine learning and protein allostery S Xiao, GM Verkhivker, P Tao Trends in Biochemical Sciences 48 (4), 375-390, 2022 | 18 | 2022 |
| Analyzing and Predicting the Viscosity of Polymer Nanocomposites in the Conditions of Temperature, Shear Rate, and Nanoparticles Loading with Molecular Dynamics Simulations and … H Li, H Tian, Y Chen, S Xiao, Y Gao, X Zhao, L Zhang The Journal of Physical Chemistry B 127 (15), 3596-3605, 2023 | 14 | 2023 |
| Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling … GM Verkhivker, M Alshahrani, G Gupta, S Xiao, P Tao Physical Chemistry Chemical Physics 25, 21245-21266, 2023 | 11 | 2023 |
| LAST: Latent Space Assisted Adaptive Sampling for Protein Trajectories H Tian, X Jiang, S Xiao, H La Force, EC Larson, P Tao Journal of Chemical Information and Modeling 63 (1), 67-75, 2022 | 11 | 2022 |
| From Deep Mutational Mapping of Allosteric Protein Landscapes to Deep Learning of Allostery and Hidden Allosteric Sites: Zooming in on “Allosteric Intersection” of Biochemical … G Verkhivker, M Alshahrani, G Gupta, S Xiao, P Tao International Journal of Molecular Sciences 24 (9), 7747, 2023 | 10 | 2023 |
| Integration of a Randomized Sequence Scanning Approach in AlphaFold2 and Local Frustration Profiling of Conformational States Enable Interpretable Atomistic Characterization of … N Raisinghani, M Alshahrani, G Gupta, H Tian, S Xiao, P Tao, ... Journal of Chemical Theory and Computation 20 (12), 5317–5336, 2024 | 8* | 2024 |
| Comparative analysis of conformational dynamics and systematic characterization of cryptic pockets in the SARS-CoV-2 omicron BA. 2, BA. 2.75 and XBB. 1 spike complexes with the … M Alshahrani, G Gupta, S Xiao, P Tao, G Verkhivker Viruses 15 (10), 2073, 2023 | 8 | 2023 |
| AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between Convergent Mutational … N Raisinghani, M Alshahrani, G Gupta, S Xiao, P Tao, G Verkhivker The Journal of Physical Chemistry B 128 (19), 4696–4715, 2024 | 5 | 2024 |
| 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 … N Raisinghani, M Alshahrani, G Gupta, S Xiao, P Tao, G Verkhivker Journal of Chemical Information and Modeling 64 (5), 1657–1681, 2024 | 5 | 2024 |
| Exploring conformational landscapes and binding mechanisms of convergent evolution for the SARS-CoV-2 spike Omicron variant complexes with the ACE2 receptor using AlphaFold2 … N Raisinghani, M Alshahrani, G Gupta, S Xiao, P Tao, G Verkhivker Physical Chemistry Chemical Physics 26 (25), 17720-17744, 2024 | 4 | 2024 |
| Assessments of Variational Autoencoder in Protein Conformation Exploration S Xiao, Z Song, H Tian, P Tao Journal of Computational Biophysics and Chemistry 22 (4), 489-501, 2023 | 3 | 2023 |
| Probing Functional Allosteric States and Conformational Ensembles of the Allosteric Protein Kinase States and Mutants: Atomistic Modeling and Comparative Analysis of AlphaFold2 … N Raisinghani, M Alshahrani, G Gupta, H Tian, S Xiao, P Tao, ... The Journal of Physical Chemistry B 128 (45), 11088-11107, 2024 | 2 | 2024 |
| β‐sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini S Xiao, MT Ibrahim, GM Verkhivker, BD Zoltowski, P Tao Journal of Computational Chemistry 45 (17), 1493-1504, 2024 | 2 | 2024 |
| AlphaFold2-Enabled Atomistic Modeling of Epistatic Binding Mechanisms for the SARS-CoV-2 Spike Omicron XBB. 1.5, EG. 5 and FLip Variants: Convergent Evolution Hotspots … N Raisinghani, M Alshahrani, G Gupta, S Xiao, P Tao, G Verkhivker bioRxiv, 2023.12. 11.571185, 2023 | 1 | 2023 |
| Accurate Characterization of the Allosteric Energy Landscapes, Binding Hotspots and Long-Range Communications for KRAS Complexes with Effector Proteins: Integrative Approach … S Xiao, M Alshahrani, G Hu, P Tao, G Verkhivker bioRxiv, 2025.01. 27.635141, 2025 | | 2025 |
Peng Tao (陶鹏)Associate Professor, Chemistry Department, Southern Methodist UniversityPotvrđena adresa e-pošte na smu.edu