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RESEARCH PAPER · The Journal of Physical Chemistry B · 2020

Deciphering the Allosteric Process of the Phaeodactylum tricornutum Aureochrome 1a LOV Domain

Hao Tian, Francesco Trozzi, Brian D. Zoltowski, Peng Tao

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30 direct citing papers in this saved network. Explore the next layer with second-order citations.

Open in your workspace →Saved 2026-10-14 · complete coverage
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42 direct citing works

Deciphering the Allosteric Process of the Phaeodactylum tricornutum Aureochrome 1a LOV DomainOriginalReproducibility of volumetric measurements of normal maculae with the Heidelberg retina tomograph24The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry3The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry6The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry2PASSer: prediction of allosteric sites server79UMAP as a Dimensionality Reduction Tool for Molecular Dynamics Simulations of Biomacromolecules: A Comparison Study122Transmission of light signals from the light-oxygen-voltage core via the hydrophobic region of the β-sheet surface in aureochrome-19Automated Parsing of Flexible Molecular Systems using Principal Component Analysis and K-Means Clustering Techniques0Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE6Rheological mechanism of polymer nanocomposites filled with spherical nanoparticles: Insight from molecular dynamics simulation17PASSer2.0: Accurate Prediction of Protein Allosteric Sites Through Automated Machine Learning0PASSer2.0: Accurate Prediction of Protein Allosteric Sites Through Automated Machine Learning1Dynamics of hydrogen bonds in the secondary structures of allosteric protein Avena Sativa phototropin 115Sensing and Signalling in Diatom Responses to Abiotic Cues25High-throughput screening of tribological properties of monolayer films using molecular dynamics and machine learning18Markov State Study of Electrostatic Channeling within the Tricarboxylic Acid Cycle Supercomplex1Light sensing in the Ocean : studying diatom phytochrome photoreceptors0PASSer2.0: Accurate Prediction of Protein Allosteric Sites Through Automated Machine Learning61In Silico Study of the Acquired Resistance Caused by the Secondary Mutations of KRAS G12C Protein Using Long Time Molecular Dynamics Simulation and Markov State Model Analysis19ADMETboost: a web server for accurate ADMET prediction121LAST: Latent Space-Assisted Adaptive Sampling for Protein Trajectories20Analyzing and Predicting the Viscosity of Polymer Nanocomposites in the Conditions of Temperature, Shear Rate, and Nanoparticle Loading with Molecular Dynamics Simulations and Machine Learning26PASSer: fast and accurate prediction of protein allosteric sites70Network analysis of chromophore binding site in LOV domain0PASSerRank: Prediction of allosteric sites with learning to rank40Markov State Models: To Optimize or Not to Optimize19An ab initio information-theoretic approach to proteins and protein-ligand interactions1A Knockout of the Photoreceptor PtAureo1a Results in Altered Diel Expression of Diatom Clock Components14Decoding Allostery: How Interactions Lock S100B Conformations and What K55A Mutation Teaches Us0From atoms to algae: Aureochromes in photobiology and optogenetics1

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30 direct citing papers saved.

  1. Reproducibility of volumetric measurements of normal maculae with the Heidelberg retina tomograph

    British Journal of Ophthalmology · 1998-08-01

    Hadi Zambarakji, J E Evans, Winfried M. K. Amoaku, Stephen A Vernon

    Read original paper ↗ ·

  2. The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry

    The Journal of Physical Chemistry C · 2020-11-05

    Andrew L. Ferguson, Johannes Hachmann, Thomas F. Miller, Jim Pfaendtner

    Read original paper ↗ ·

  3. The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry

    The Journal of Physical Chemistry B · 2020-11-05

    Andrew L. Ferguson, Johannes Hachmann, Thomas F. Miller, Jim Pfaendtner

    Read original paper ↗ ·

  4. The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry

    The Journal of Physical Chemistry A · 2020-11-05

    Andrew L. Ferguson, Johannes Hachmann, Thomas F. Miller, Jim Pfaendtner

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  5. PASSer: prediction of allosteric sites server

    Machine Learning Science and Technology · 2021-02-16

    Hao Tian, Xi Jiang, Peng Tao

    Read original paper ↗ ·

  6. UMAP as a Dimensionality Reduction Tool for Molecular Dynamics Simulations of Biomacromolecules: A Comparison Study

    The Journal of Physical Chemistry B · 2021-05-11

    Francesco Trozzi, Xinlei Wang, Peng Tao

    Read original paper ↗ ·

  7. Transmission of light signals from the light-oxygen-voltage core via the hydrophobic region of the β-sheet surface in aureochrome-1

    Scientific Reports · 2021-06-07

    Hiroto Nakajima, Itsuki Kobayashi, Yumiko Adachi, Osamu Hisatomi

    Read original paper ↗ ·

  8. Automated Parsing of Flexible Molecular Systems using Principal Component Analysis and K-Means Clustering Techniques

    Unknown journal · 2021-06-28

    Matthew Nwerem

    Read original paper ↗ ·

  9. Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE

    PLoS Computational Biology · 2021-07-26

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

    Read original paper ↗ ·

  10. Rheological mechanism of polymer nanocomposites filled with spherical nanoparticles: Insight from molecular dynamics simulation

    Polymer · 2021-08-25

    Haoxiang Li, Haoyu Wu, Wenfeng Zhang, Xiuying Zhao, Liqun Zhang, Yangyang Gao

    Read original paper ↗ ·

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

    Unknown journal · 2021-10-12

    Sian Xiao, Hao Tian, Peng Tao

    Read original paper ↗ ·

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

    Unknown journal · 2021-11-09

    Sian Xiao, Hao Tian, Peng Tao

    Read original paper ↗ ·

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

    Computational and Structural Biotechnology Journal · 2021-12-07

    Mayar Tarek Ibrahim, Francesco Trozzi, Peng Tao

    Read original paper ↗ ·

  14. Sensing and Signalling in Diatom Responses to Abiotic Cues

    Springer eBooks · 2022-01-01

    Marianne J. Jaubert, Carole Duchêne, Peter G. Kroth, Alessandra Rogato, Jean‐Pierre Bouly, Angela Falciatore

    Read original paper ↗ ·

  15. High-throughput screening of tribological properties of monolayer films using molecular dynamics and machine learning

    The Journal of Chemical Physics · 2022-02-21

    Co D. Quach, Justin Gilmer, Daniel Pert, Akanke Mason-Hogans, Christopher R. Iacovella, Peter T. Cummings, Clare McCabe

    Read original paper ↗ ·

  16. Markov State Study of Electrostatic Channeling within the Tricarboxylic Acid Cycle Supercomplex

    ACS Nanoscience Au · 2022-06-07

    Yan Xie, Shelley D. Minteer, Scott A. Banta, Scott Calabrese Barton

    Read original paper ↗ ·

  17. Light sensing in the Ocean : studying diatom phytochrome photoreceptors

    Unknown journal · 2022-06-28

    Carole Duchêne

    Read original paper ↗ ·

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

    Frontiers in Molecular Biosciences · 2022-07-11

    Sian Xiao, Hao Tian, Peng Tao

    Read original paper ↗ ·

  19. In Silico Study of the Acquired Resistance Caused by the Secondary Mutations of KRAS G12C Protein Using Long Time Molecular Dynamics Simulation and Markov State Model Analysis

    International Journal of Molecular Sciences · 2022-11-10

    Gao Tu, Qing Liu, Yue Qiu, Elaine Lai‐Han Leung, Xiaojun Yao

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  20. ADMETboost: a web server for accurate ADMET prediction

    Journal of Molecular Modeling · 2022-12-01

    Hao Tian, Rajas Ketkar, Peng Tao

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  21. LAST: Latent Space-Assisted Adaptive Sampling for Protein Trajectories

    Journal of Chemical Information and Modeling · 2022-12-06

    Hao Tian, Xi Jiang, Sian Xiao, Hunter La Force, Eric C. Larson, Peng Tao

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  22. Analyzing and Predicting the Viscosity of Polymer Nanocomposites in the Conditions of Temperature, Shear Rate, and Nanoparticle Loading with Molecular Dynamics Simulations and Machine Learning

    The Journal of Physical Chemistry B · 2023-04-05

    Haoxiang Li, Hao Tian, Yewei Chen, Sian Xiao, Xiuying Zhao, Yangyang Gao, Liqun Zhang

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  23. PASSer: fast and accurate prediction of protein allosteric sites

    Nucleic Acids Research · 2023-04-27

    Hao Tian, Sian Xiao, Xi Jiang, Peng Tao

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  24. Network analysis of chromophore binding site in LOV domain

    Computers in Biology and Medicine · 2023-05-04

    Rishab Panda, Pritam Kumar Panda, Janarthanan Krishnamoorthy, Rajiv K. Kar

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  25. PASSerRank: Prediction of allosteric sites with learning to rank

    Journal of Computational Chemistry · 2023-08-10

    Hao Tian, Sian Xiao, Xi Jiang, Peng Tao

    Read original paper ↗ ·

  26. Markov State Models: To Optimize or Not to Optimize

    Journal of Chemical Theory and Computation · 2024-01-02

    Robert E. Arbon, Yanchen Zhu, Antonia S. J. S. Mey

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  27. An ab initio information-theoretic approach to proteins and protein-ligand interactions

    bioRxiv (Cold Spring Harbor Laboratory) · 2024-03-08

    Deep Nath, Rajdeep Kaur Grewal, Devrani Mitra, Soumen Roy

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  28. A Knockout of the Photoreceptor PtAureo1a Results in Altered Diel Expression of Diatom Clock Components

    Plants · 2024-05-25

    Shvaita Madhuri, Lepetit Bernard, Alexander Helmut Fürst, Peter G. Kroth

    Read original paper ↗ ·

  29. Decoding Allostery: How Interactions Lock S100B Conformations and What K55A Mutation Teaches Us

    Journal of Chemical Information and Modeling · 2025-11-21

    Riya Samanta, Xinhao Zhuang, Manuel Gondolesi, Kristen M. Varney, David J. Weber, Silvina Matysiak

    Read original paper ↗ ·

  30. From atoms to algae: Aureochromes in photobiology and optogenetics

    Algal Research · 2026-05-01

    Debarshi Bose, Abhilasha Ghosh, Madhurima Khamaru, Devrani Mitra

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