Peng Tao

Biochemistry, Genetics and Molecular BiologyImmunology and MicrobiologyMaterials Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 41 papers. Top paper: “PASSer: Prediction of Allosteric Sites Server”.

PASSer: Prediction of Allosteric Sites Server

ChemRxiv(2020)10.26434/chemrxiv.13360535.v2

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4 citations

Xi Jiang, Peng Tao, Hao Tian

Explore Protein Conformational Space With Variational Autoencoder

Frontiers in Molecular Biosciences(2021)10.3389/fmolb.2021.781635

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0DataRank · unranked

50 citations

Xi Jiang, Francesco Trozzi, Sian Xiao, Eric C. Larson, Peng Tao +1 more

Mechanistic Basis of OXA-48-like β-Lactamases’ Hydrolysis of Carbapenems

ACS Infectious Diseases(2021)10.1021/acsinfecdis.0c00798

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43 citations

Liya Hu, Banumathi Sankaran, Feng Wang, Peng Tao, B. V. Venkataram Prasad +2 more

SSnet: A Deep Learning Approach for Protein-Ligand Interaction Prediction

International Journal of Molecular Sciences(2021)10.3390/ijms22031392

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49 citations

Xingming Qu, Francesco Trozzi, Mohamed Elsaied, Nischal Karki, Peng Tao +4 more

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(2021)10.3390/ijms22041573

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41 citations

Niraj Verma, Francesco Trozzi, Peng Tao, Elfi Kraka, Brian D. Zoltowski +1 more

Dynamics of hydrogen bonds in the secondary structures of allosteric protein Avena Sativa phototropin 1

Computational and Structural Biotechnology Journal(2021)10.1016/j.csbj.2021.11.038

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20 citations

Francesco Trozzi, Peng Tao, Mayar Tarek Ibrahim

QM/MM modeling of class A β-lactamases reveals distinct acylation pathways for ampicillin and cefalexin

Organic & Biomolecular Chemistry(2021)10.1039/d1ob01593a

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7 citations

Francesco Trozzi, Timothy Palzkill, Peng Tao, Zilin Song

Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE

PLoS Computational Biology(2021)10.1371/journal.pcbi.1009168

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6 citations

Feng Wang, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao, Francesco Trozzi

PASSer2.0: Accurate Prediction of Protein Allosteric Sites Through Automated Machine Learning

ChemRxiv(2021)10.26434/chemrxiv-2021-q4319-v2

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0DataRank · unranked

1 citations

Hao Tian, Peng Tao, Sian Xiao

PASSer2.0: Accurate Prediction of Protein Allosteric Sites Through Automated Machine Learning

(2021)10.33774/chemrxiv-2021-q4319-v2

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0DataRank · unranked

1 citations

Hao Tian, Peng Tao, Sian Xiao

PASSer2.0: Accurate Prediction of Protein Allosteric Sites Through Automated Machine Learning

ChemRxiv(2021)10.26434/chemrxiv-2021-q4319

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0DataRank · unranked

1 citations

Hao Tian, Peng Tao, Sian Xiao

PASSer2.0: Accurate Prediction of Protein Allosteric Sites Through Automated Machine Learning

(2021)10.33774/chemrxiv-2021-q4319

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0DataRank · unranked

0 citations

Hao Tian, Peng Tao, Sian Xiao

PASSer2.0: Accurate Prediction of Protein Allosteric Sites Through Automated Machine Learning

Frontiers in Molecular Biosciences(2022)10.3389/fmolb.2022.879251

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63 citations

Hao Tian, Peng Tao, Sian Xiao

Machine learning and protein allostery

Trends in Biochemical Sciences(2022)10.1016/j.tibs.2022.12.001

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33 citations

Gennady M. Verkhivker, Peng Tao, Sian Xiao

Unveiling the structural features that regulate carbapenem deacylation in KPC-2 through QM/MM and interpretable machine learning

Physical Chemistry Chemical Physics(2022)10.1039/d2cp03724f

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7 citations

Zilin Song, Hao Tian, Timothy Palzkill, Peng Tao, Chao Yin

Assessments of Variational Autoencoder in Protein Conformation Exploration

ChemRxiv(2022)10.26434/chemrxiv-2022-g2c00

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1 citations

Zilin Song, Hao Tian, Peng Tao, Sian Xiao

PASSer: fast and accurate prediction of protein allosteric sites

Nucleic Acids Research(2023)10.1093/nar/gkad303

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0DataRank · unranked

69 citations

Sian Xiao, Xi Jiang, Peng Tao, Hao Tian

PASSerRank: Prediction of allosteric sites with learning to rank

Journal of Computational Chemistry(2023)10.1002/jcc.27193

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0DataRank · unranked

43 citations

Sian Xiao, Xi Jiang, Peng Tao, Hao Tian

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)10.1021/acs.jcim.3c00778

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43 citations

Mohammed Alshahrani, Grace Gupta, Peng Tao, Gennady M. Verkhivker, Sian Xiao

Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.2c01634

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37 citations

Mohammed Alshahrani, Fang Bai, Peng Tao, Gennady M. Verkhivker, Steve Agajanian

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(2023)10.1039/d3cp02042h

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16 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker

From Deep Mutational Mapping of Allosteric Protein Landscapes to Deep Learning of Allostery and Hidden Allosteric Sites: Zooming in on “Allosteric Intersection” of Biochemical and Big Data Approaches

International Journal of Molecular Sciences(2023)10.3390/ijms24097747

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0DataRank · unranked

15 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker

Assessments of Variational Autoencoder in Protein Conformation Exploration

Journal of Computational Biophysics and Chemistry(2023)10.1142/s2737416523500217

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12 citations

Zilin Song, Hao Tian, Peng Tao, Sian Xiao

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 ACE2 Host Receptor: Confluence of Binding and Structural Plasticity in Mediating Networks of Conserved Allosteric Sites

Viruses(2023)10.3390/v15102073

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9 citations

Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker, Mohammed Alshahrani

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 (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.11.557205

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0DataRank · unranked

0 citations

Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker, Mohammed Alshahrani

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 (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.03.539337

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0DataRank · unranked

0 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, 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 (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.20.541592

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0DataRank · unranked

0 citations

Mohammed Alshahrani, Grace Gupta, Peng Tao, Gennady M. Verkhivker, Sian Xiao

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 (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.18.567697

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0DataRank · unranked

0 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

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 (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.11.571185

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0 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

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

鐵と鋼 : 日本鐡鋼協會々誌(2023)10.1101/2023.12.22.573121

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0 citations

Mayar Tarek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao, Sian Xiao

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)10.1021/acs.jctc.4c00222

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17 citations

Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao +2 more

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)10.1021/acs.jpcb.4c01341

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17 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

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(2024)10.1039/d4cp01372g

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13 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

β‐sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini

Journal of Computational Chemistry(2024)10.1002/jcc.27344

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5 citations

Mayar Tarek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao, Sian Xiao

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)10.1021/acs.jcim.3c01857

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0DataRank · unranked

7 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

Probing Functional Allosteric States and Conformational Ensembles of the Allosteric Protein Kinase States and Mutants: Atomistic Modeling and Comparative Analysis of AlphaFold2, OmegaFold, and AlphaFlow Approaches and Adaptations

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c04985

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5 citations

Mohammed Merae Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao +2 more

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 (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.02.587850

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7 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

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 (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.15.580591

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0DataRank · unranked

5 citations

Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao +2 more

Exploring binding and allosteric energy landscapes for the KRAS interactions with effector proteins using Markov state modeling of conformational ensembles and allosteric network modeling

Protein Science(2025)10.1002/pro.70228

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9 citations

Mohammed Merae Alshahrani, Guang Hu, Peng Tao, Gennady M. Verkhivker, Sian Xiao

Structural Plasticity and Functional Dynamics of Pigeon Cryptochrome 4 as Avian Magnetoreceptor

Journal of Molecular Biology(2025)10.1016/j.jmb.2025.169233

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3 citations

Palanisamy Kandhan, Brian D. Zoltowski, Peng Tao, Chuanye Xiong

Efficient Sampling of Protein Trajectories with Conditional Diffusion Models

ChemRxiv(2025)10.26434/chemrxiv-2025-xq07m

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1 citations

Zongmin Ma, Eleanor Smith, Palanisamy Kandhan, Peng Tao, Chuanye Xiong