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RESEARCH PAPER · Scientific Reports · 2018

Understanding Colour Tuning Rules and Predicting Absorption Wavelengths of Microbial Rhodopsins by Data-Driven Machine-Learning Approach

Masayuki Karasuyama, Keiichi Inoue, Ryoko Nakamura, Hideki Kandori, Ichiro Takeuchi

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Understanding Colour Tuning Rules and Predicting Absorption Wavelengths of Microbial Rhodopsins by Data-Driven Machine-Learning ApproachOriginalKalium Permanganat: Termodinamika Mengenai Transport Ionik dalam Air29a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement57Enzymerhodopsins: novel photoregulated catalysts for optogenetics61Active Learning of Bayesian Linear Models with High-Dimensional Binary Features by Parameter Confidence-Region Estimation1RubyACRs, nonalgal anion channelrhodopsins with highly red-shifted absorption75Active Learning for Level Set Estimation Under Input Uncertainty and Its Extensions7On the Automatic Construction of QM/MM Models for Biological Photoreceptors: Rhodopsins as Model Systems7NeoR, a near-infrared absorbing rhodopsin121Insights into the Protein Functions and Absorption Wavelengths of Microbial Rhodopsins22High Dimensional Level Set Estimation with Bayesian Neural Network1Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins20Sub-picosecond C = C bond photo-isomerization: evidence for the role of excited state mixing10Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design33Random Embeddings and Linear Regression can Predict Protein Function2High Dimensional Level Set Estimation with Bayesian Neural Network6Evaluation of machine learning-based applications in forecasting the performance of single effect absorption chiller network29Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol4Far-Red Absorbing Rhodopsins, Insights From Heterodimeric Rhodopsin-Cyclases19Mutational analyses identify a single amino acid critical for colour tuning in proteorhodopsins4Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol19Earliest Photic Zone Niches Probed by Ancestral Microbial Rhodopsins23Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering34The binding of secondary chromophore for thermally stable rhodopsin makes more stable with temperature7PhISCO: a simple method to infer phenotypes from protein sequences0Impact of protein–chromophore interaction on the retinal excited state and photocycle of Gloeobacter rhodopsin: role of conserved tryptophan residues1Induction effects on the absorption maxima of photoreceptor proteins2Ion-pumping microbial rhodopsin protein classification by machine learning approach4Fine spectral tuning of a flavin-binding fluorescent protein for multicolor imaging21Optogenetic Methods in Plant Biology32Raman Optical Activity of Retinal Chromophore in Sensory Rhodopsin II8Photochemistry of the Retinal Chromophore in Microbial Rhodopsins16Efficient model selection for predictive pattern mining model by safe pattern pruning1Opto-electronic feedback control of membrane potential for real-time control of action potentials12Discovering genotype–phenotype relationships with machine learning and the Visual Physiology Opsin Database ( VPOD )12Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins14Tetherless Optical Neuromodulation: Wavelength from Orange-red to Mid-infrared10Associating protein sequence positions with the modulation of quantitative phenotypes0Deep dive into the diversity and properties of rhodopsins in actinomycetes of the family Geodermatophilaceae0RhoMax: Computational Prediction of Rhodopsin Absorption Maxima Using Geometric Deep Learning6Rhodopsin‐based light‐harvesting system for sustainable synthetic biology9Sensing Light Underwater0Reconstructing Early Microbial Life23Guest-Mediated Modulation of Photophysical Pathways in a Coronene Bisimide Cyclophane9Molecular Mechanisms Underlying the Spectral Shift in Zebrafish Cone Opsins2Structural changes of Natronomonas pharaonis halorhodopsin in its late photocycle revealed by solid-state NMR spectroscopy1Mode-Specific Photoresponse of Retinal Protonated Schiff Base Isomers in the Reversible Photochromic Reactions of Microbial and Animal Rhodopsins3Deep dive into the diversity and properties of rhodopsins in actinomycetes of the family Geodermatophilaceae0Origin of the red-shifted absorption maximum in channelrhodopsin Chrimson1Photofunctional cyclophane host–guest systems24Blue-shifted ancyromonad channelrhodopsins for multiplex optogenetics0Blue-shifted ancyromonad channelrhodopsins for multiplex optogenetics0Two Decades of Optogenetic Tools: A Retrospective and a Look Ahead8Blue-shifted ancyromonad channelrhodopsins for multiplex optogenetics0Blue-shifted ancyromonad channelrhodopsins for multiplex optogenetics4Functional characterization of red-shifted rhodopsin channels from giant viruses explored by a machine-learning model for long-wavelength optogenetics0Following Flavin’s Vibrational Modes to Probe Anharmonicities and Low-Lying Conical Intersections6FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications3Accessible and robust machine learning approaches to improve the opsin genotype-phenotype map2Computational design of microbial and animal rhodopsin soluble analogues0AI-enabled rhodopsin design for blue-light enhanced bacterial growth0Rhobot-Screen: an integrated robotic platform for functional screening of rhodopsin variants0

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  1. Kalium Permanganat: Termodinamika Mengenai Transport Ionik dalam Air

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  2. a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement

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  3. Enzymerhodopsins: novel photoregulated catalysts for optogenetics

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  4. Active Learning of Bayesian Linear Models with High-Dimensional Binary Features by Parameter Confidence-Region Estimation

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  5. RubyACRs, nonalgal anion channelrhodopsins with highly red-shifted absorption

    Proceedings of the National Academy of Sciences · 2020-09-01

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  6. Active Learning for Level Set Estimation Under Input Uncertainty and Its Extensions

    Neural Computation · 2020-10-20

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  7. On the Automatic Construction of QM/MM Models for Biological Photoreceptors: Rhodopsins as Model Systems

    Challenges and advances in computational chemistry and physics · 2020-10-27

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  8. NeoR, a near-infrared absorbing rhodopsin

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  9. Insights into the Protein Functions and Absorption Wavelengths of Microbial Rhodopsins

    The Journal of Physical Chemistry B · 2020-11-25

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  10. High Dimensional Level Set Estimation with Bayesian Neural Network

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    Huong Ha, Sunil Gupta, Santu Rana, Svetha Venkatesh

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  11. Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins

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  12. Sub-picosecond C = C bond photo-isomerization: evidence for the role of excited state mixing

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  13. Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design

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  14. Random Embeddings and Linear Regression can Predict Protein Function

    arXiv (Cornell University) · 2021-04-25

    Tianyu Lu, Alex Xijie Lu, Alan M Moses

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  15. High Dimensional Level Set Estimation with Bayesian Neural Network

    Proceedings of the AAAI Conference on Artificial Intelligence · 2021-05-18

    Huong Ha, Sunil Gupta, Santu Rana, Svetha Venkatesh

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  16. Evaluation of machine learning-based applications in forecasting the performance of single effect absorption chiller network

    Thermal Science and Engineering Progress · 2021-10-13

    Farshad Panahizadeh, Mahdi Hamzehei, Mahmood Farzaneh-Gord, Álvaro Antônio Ochoa Villa

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  17. Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol

    Topics in current chemistry collections · 2022-01-01

    Laura Pedraza‐González, Leonardo Barneschi, Daniele Padula, Luca De Vico, Massimo Olivucci

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  18. Far-Red Absorbing Rhodopsins, Insights From Heterodimeric Rhodopsin-Cyclases

    Frontiers in Molecular Biosciences · 2022-01-21

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  19. Mutational analyses identify a single amino acid critical for colour tuning in proteorhodopsins

    FEBS Letters · 2022-01-28

    Jin‐gon Shim, Na‐rae Kang, Kimleng Chuon, Shin‐Gyu Cho, Seanghun Meas, Kwang‐Hwan Jung

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  20. Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol

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  21. Earliest Photic Zone Niches Probed by Ancestral Microbial Rhodopsins

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  22. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

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  23. The binding of secondary chromophore for thermally stable rhodopsin makes more stable with temperature

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  24. PhISCO: a simple method to infer phenotypes from protein sequences

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  25. Impact of protein–chromophore interaction on the retinal excited state and photocycle of Gloeobacter rhodopsin: role of conserved tryptophan residues

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  26. Induction effects on the absorption maxima of photoreceptor proteins

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  27. Ion-pumping microbial rhodopsin protein classification by machine learning approach

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  31. Photochemistry of the Retinal Chromophore in Microbial Rhodopsins

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  32. Efficient model selection for predictive pattern mining model by safe pattern pruning

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  35. Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins

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  36. Tetherless Optical Neuromodulation: Wavelength from Orange-red to Mid-infrared

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  37. Associating protein sequence positions with the modulation of quantitative phenotypes

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  38. Deep dive into the diversity and properties of rhodopsins in actinomycetes of the family Geodermatophilaceae

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  39. RhoMax: Computational Prediction of Rhodopsin Absorption Maxima Using Geometric Deep Learning

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  45. Structural changes of Natronomonas pharaonis halorhodopsin in its late photocycle revealed by solid-state NMR spectroscopy

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  46. Mode-Specific Photoresponse of Retinal Protonated Schiff Base Isomers in the Reversible Photochromic Reactions of Microbial and Animal Rhodopsins

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  47. Deep dive into the diversity and properties of rhodopsins in actinomycetes of the family Geodermatophilaceae

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  48. Origin of the red-shifted absorption maximum in channelrhodopsin Chrimson

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  49. Photofunctional cyclophane host–guest systems

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  50. Blue-shifted ancyromonad channelrhodopsins for multiplex optogenetics

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