Peng Tao

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 70

Top Topics

Electron Transfer

Machine Learning

Chronic Myeloid Leukemia

Top Venues

bioRxiv : the preprint server for biology

Journal of chemical information and modeling

Physical chemistry chemical physics : PCCP

Journal of computational chemistry

This page only lists publications with an associated author ORCID identifier.

Publications

Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
Predicting Functional Conformational Ensembles and Binding Mechanisms of Convergent Evolution for SARS-CoV-2 Spike Omicron Variants Using AlphaFold2 Sequence Scanning Adaptations and Molecular Dynamics Simulations. bioRxiv : the preprint server for biology (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
Prediction of Conformational Ensembles and Structural Effects of State-Switching Allosteric Mutants in the Protein Kinases Using Comparative Analysis of AlphaFold2 Adaptations with Sequence Masking and Shallow Subsampling. bioRxiv : the preprint server for biology (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
Exploring conformational landscapes and binding mechanisms of convergent evolution for the SARS-CoV-2 spike Omicron variant complexes with the ACE2 receptor using AlphaFold2-based structural ensembles and molecular dynamics simulations. Physical chemistry chemical physics : PCCP 26 (25) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
Integration of a Randomized Sequence Scanning Approach in AlphaFold2 and Local Frustration Profiling of Conformational States Enable Interpretable Atomistic Characterization of Conformational Ensembles and Detection of Hidden Allosteric States in the ABL1 Protein Kinase. Journal of chemical theory and computation 20 (12) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
Exploring conformational landscapes and binding mechanisms of convergent evolution for the SARS-CoV-2 spike Omicron variant complexes with the ACE2 receptor using AlphaFold2-based structural ensembles and molecular dynamics simulations. Physical chemistry chemical physics : PCCP (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
Interpretable Atomistic Prediction and Functional Analysis of Conformational Ensembles and Allosteric States in Protein Kinases Using AlphaFold2 Adaptation with Randomized Sequence Scanning and Local Frustration Profiling. bioRxiv : the preprint server for biology (2024)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. Journal of computational chemistry (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
Predicting Functional Conformational Ensembles and Binding Mechanisms of Convergent Evolution for SARS-CoV-2 Spike Omicron Variants Using AlphaFold2 Sequence Scanning Adaptations and Molecular Dynamics Simulations. bioRxiv : the preprint server for biology (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. Journal of chemical information and modeling 64 (5) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. Journal of chemical information and modeling 64 (5) (2024)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. Journal of computational chemistry 45 (17) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between Convergent Mutational Hotspots that Control ACE2 Affinity. The journal of physical chemistry. B 128 (19) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
Predicting Functional Conformational Ensembles and Binding Mechanisms of Convergent Evolution for SARS-CoV-2 Spike Omicron Variants Using AlphaFold2 Sequence Scanning Adaptations and Molecular Dynamics Simulations. bioRxiv : the preprint server for biology (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between Convergent Mutational Hotspots that Control ACE2 Affinity. The journal of physical chemistry. B 128 (19) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
Exploring conformational landscapes and binding mechanisms of convergent evolution for the SARS-CoV-2 spike Omicron variant complexes with the ACE2 receptor using AlphaFold2-based structural ensembles and molecular dynamics simulations. Physical chemistry chemical physics : PCCP (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between Convergent Mutational Hotspots that Control ACE2 Affinity. The journal of physical chemistry. B (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. Journal of chemical information and modeling (2024)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. Journal of computational chemistry 45 (17) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
Exploring conformational landscapes and binding mechanisms of convergent evolution for the SARS-CoV-2 spike Omicron variant complexes with the ACE2 receptor using AlphaFold2-based structural ensembles and molecular dynamics simulations. Physical chemistry chemical physics : PCCP 26 (25) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
Integration of a Randomized Sequence Scanning Approach in AlphaFold2 and Local Frustration Profiling of Conformational States Enable Interpretable Atomistic Characterization of Conformational Ensembles and Detection of Hidden Allosteric States in the ABL1 Protein Kinase. Journal of chemical theory and computation (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. Journal of chemical information and modeling 64 (5) (2024)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. Journal of computational chemistry 45 (17) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
Interpretable Atomistic Prediction and Functional Analysis of Conformational Ensembles and Allosteric States in Protein Kinases Using AlphaFold2 Adaptation with Randomized Sequence Scanning and Local Frustration Profiling. bioRxiv : the preprint server for biology (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
Integration of a Randomized Sequence Scanning Approach in AlphaFold2 and Local Frustration Profiling of Conformational States Enable Interpretable Atomistic Characterization of Conformational Ensembles and Detection of Hidden Allosteric States in the ABL1 Protein Kinase. Journal of chemical theory and computation (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
Integration of a Randomized Sequence Scanning Approach in AlphaFold2 and Local Frustration Profiling of Conformational States Enable Interpretable Atomistic Characterization of Conformational Ensembles and Detection of Hidden Allosteric States in the ABL1 Protein Kinase. Journal of chemical theory and computation 20 (12) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
Interpretable Atomistic Prediction and Functional Analysis of Conformational Ensembles and Allosteric States in Protein Kinases Using AlphaFold2 Adaptation with Randomized Sequence Scanning and Local Frustration Profiling. bioRxiv : the preprint server for biology (2024)
Keerthi Krishnan, Hao Tian, Peng Tao, Gennady M Verkhivker
Probing conformational landscapes and mechanisms of allosteric communication in the functional states of the ABL kinase domain using multiscale simulations and network-based mutational profiling of allosteric residue potentials. The Journal of chemical physics 157 (24) (2023)
Sian Xiao, Mohammed Alshahrani, Grace Gupta, Peng Tao, Gennady M Verkhivker
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. Journal of chemical information and modeling (2023)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
Microsecond Molecular Dynamics Simulations and Markov State Models of Mutation-Induced Allosteric Mechanisms for the Light-Oxygen-Voltage 2 Protein : Revealing Structural Basis of Signal Transmission Induced by Photoactivation of the Light Protein State. bioRxiv : the preprint server for biology (2023)
Hao Tian, Sian Xiao, Xi Jiang, Peng Tao
PASSerRank: Prediction of allosteric sites with learning to rank. Journal of computational chemistry (2023)
Chao Yin, Zilin Song, Hao Tian, Timothy G Palzkill, Peng Tao
Unveiling the structural features that regulate carbapenem deacylation in KPC-2 through QM/MM and interpretable machine learning. Physical chemistry chemical physics : PCCP 25 (2) (2023)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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 Cooperate to Control Stability and Conformational Adaptability in Balancing ACE2 Binding and Antibody Resistance. bioRxiv : the preprint server for biology (2023)
Gennady M Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao
Probing Conformational Landscapes of Binding and Allostery in the SARS-CoV-2 Omicron Variant Complexes Using Microsecond Atomistic Simulations and Perturbation-Based Profiling Approaches: Hidden Role of Omicron Mutations as Modulators of Allosteric Signaling and Epistatic Relationships. bioRxiv : the preprint server for biology (2023)
Gennady M Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao
Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships. Physical chemistry chemical physics : PCCP (2023)
Steve Agajanian, Mohammed Alshahrani, Fang Bai, Peng Tao, Gennady M Verkhivker
Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. Journal of chemical information and modeling 63 (5) (2023)
Gennady M Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao
Probing Conformational Landscapes of Binding and Allostery in the SARS-CoV-2 Omicron Variant Complexes Using Microsecond Atomistic Simulations and Perturbation-Based Profiling Approaches: Hidden Role of Omicron Mutations as Modulators of Allosteric Signaling and Epistatic Relationships. bioRxiv : the preprint server for biology (2023)
Steve Agajanian, Mohammed Alshahrani, Fang Bai, Peng Tao, Gennady M Verkhivker
Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. Journal of chemical information and modeling 63 (5) (2023)
Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes. bioRxiv : the preprint server for biology (2023)
Hao Tian, Sian Xiao, Xi Jiang, Peng Tao
PASSer: fast and accurate prediction of protein allosteric sites. Nucleic acids research (2023)
Steve Agajanian, Mohammed Alshahrani, Fang Bai, Peng Tao, Gennady M Verkhivker
Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. Journal of chemical information and modeling (2023)
Sian Xiao, Mohammed Alshahrani, Grace Gupta, Peng Tao, Gennady M Verkhivker
Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variants Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. bioRxiv : the preprint server for biology (2023)
Chao Yin, Zilin Song, Hao Tian, Timothy G Palzkill, Peng Tao
Unveiling the structural features that regulate carbapenem deacylation in KPC-2 through QM/MM and interpretable machine learning. Physical chemistry chemical physics : PCCP 25 (2) (2023)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
Accurate Characterization of Conformational Ensembles and Binding Mechanisms of the SARS-CoV-2 Omicron BA.2 and BA.2.86 Spike Protein with the Host Receptor and Distinct Classes of Antibodies Using AlphaFold2-Augmented Integrative Computational Modeling. bioRxiv : the preprint server for biology (2023)
Chao Yin, Zilin Song, Hao Tian, Timothy G Palzkill, Peng Tao
Unveiling the structural features that regulate carbapenem deacylation in KPC-2 through QM/MM and interpretable machine learning. Physical chemistry chemical physics : PCCP (2022)
Hao Tian, Xi Jiang, Sian Xiao, Hunter La Force, Eric C Larson, Peng Tao
LAST: Latent Space-Assisted Adaptive Sampling for Protein Trajectories. Journal of chemical information and modeling (2022)
Mayar Tarek Ibrahim, Jiyong Lee, Peng Tao
Homology modeling of Forkhead box protein C2: identification of potential inhibitors using ligand and structure-based virtual screening. Molecular diversity (2022)
Francesco Trozzi, Nischal Karki, Zilin Song, Niraj Verma, Elfi Kraka, Brian D Zoltowski, Peng Tao
Allosteric control of ACE2 peptidase domain dynamics. Organic & biomolecular chemistry 20 (17) (2022)
Mayar Tarek Ibrahim, Peng Tao
Computational investigation of peptidomimetics as potential inhibitors of SARS-CoV-2 spike protein. Journal of biomolecular structure & dynamics (2022)
Zilin Song, Francesco Trozzi, Hao Tian, Chao Yin, Peng Tao
Mechanistic Insights into Enzyme Catalysis from Explaining Machine-Learned Quantum Mechanical and Molecular Mechanical Minimum Energy Pathways. ACS Physical Chemistry Au 2 (4) (2022)
Fangyun Bai, Kin Ming Puk, Jin Liu, Hongyu Zhou, Peng Tao, Wenyong Zhou, Shouyi Wang
Sparse group selection and analysis of function-related residue for protein-state recognition. Journal of computational chemistry 43 (20) (2022)
Francesco Trozzi, Xinlei Wang, Peng Tao
UMAP as a Dimensionality Reduction Tool for Molecular Dynamics Simulations of Biomacromolecules: A Comparison Study. The journal of physical chemistry. B 125 (19) (2021)
Nischal Karki, Niraj Verma, Francesco Trozzi, Peng Tao, Elfi Kraka, Brian D Zoltowski
Predicting Potential SARS-COV-2 Drugs-In Depth Drug Database Screening Using Deep Neural Network Framework SSnet, Classical Virtual Screening and Docking. International journal of molecular sciences 22 (4) (2021)
Zilin Song, Francesco Trozzi, Timothy Palzkill, Peng Tao
QM/MM modeling of class A β-lactamases reveals distinct acylation pathways for ampicillin and cefalexin. Organic & biomolecular chemistry 19 (42) (2021)
Francesco Trozzi, Feng Wang, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE. PLoS computational biology 17 (7) (2021)
Zilin Song, Hongyu Zhou, Hao Tian, Xinlei Wang, Peng Tao
Unraveling the energetic significance of chemical events in enzyme catalysis via machine-learning based regression approach. Communications chemistry 3 (1) (2020)
Zilin Song, Hongyu Zhou, Hao Tian, Xinlei Wang, Peng Tao
Unraveling the energetic significance of chemical events in enzyme catalysis via machine-learning based regression approach. Communications chemistry 3 (1) (2020)
Hao Tian, Francesco Trozzi, Brian D Zoltowski, Peng Tao
Deciphering the Allosteric Process of the Phaeodactylum tricornutum Aureochrome 1a LOV Domain. The journal of physical chemistry. B 124 (41) (2020)
Hao Tian, Peng Tao
ivis Dimensionality Reduction Framework for Biomacromolecular Simulations. Journal of chemical information and modeling 60 (10) (2020)
Hao Tian, Peng Tao
Deciphering the protein motion of S1 subunit in SARS-CoV-2 spike glycoprotein through integrated computational methods. Journal of biomolecular structure & dynamics 39 (17) (2020)
Hongyu Zhou, Zheng Dong, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis. PLoS computational biology 15 (2) (2019)
Hamed S Hayatshahi, Emilio Ahuactzin, Peng Tao, Shouyi Wang, Jin Liu
Probing Protein Allostery as a Residue-Specific Concept via Residue Response Maps. Journal of chemical information and modeling 59 (11) (2019)
Hongyu Zhou, Feng Wang, Doran I G B Raccah, Peng Tao
Directed kinetic transition network model. The Journal of chemical physics 151 (14) (2019)
Feng Wang, Peng Tao
Exploring free energy profile of petroleum thermal cracking mechanisms. Journal of molecular modeling 26 (1) (2019)
Arshad Mehmood, Stephanie I Jones, Peng Tao, Benjamin G Janesko
An Orbital-Overlap Complement to Ligand and Binding Site Electrostatic Potential Maps. Journal of chemical information and modeling 58 (9) (2018)
Hongyu Zhou, Zheng Dong, Peng Tao
Recognition of protein allosteric states and residues: Machine learning approaches. Journal of computational chemistry 39 (20) (2018)
Collin T Zahler, Hongyu Zhou, Alireza Abdolvahabi, Rebecca L Holden, Sanaz Rasouli, Peng Tao, Bryan F Shaw
Direct Measurement of Charge Regulation in Metalloprotein Electron Transfer. Angewandte Chemie (International ed. in English) 57 (19) (2018)
Hongyu Zhou, Feng Wang, Peng Tao
t-Distributed Stochastic Neighbor Embedding Method with the Least Information Loss for Macromolecular Simulations. Journal of chemical theory and computation 14 (11) (2018)
Zheng Dong, Hongyu Zhou, Peng Tao
Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily. Protein science : a publication of the Protein Society 27 (2) (2017)
Hongyu Zhou, Peng Tao
Dynamics Sampling in Transition Pathway Space. Journal of chemical theory and computation 14 (1) (2017)
Robert Kalescky, Hongyu Zhou, Jin Liu, Peng Tao
Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery. PLoS computational biology 12 (4) (2016)