Papers citing Understanding Colour Tuning Rules and Predicting Absorption Wavelengths of Microbial Rhodopsins by Data-Driven Machine-Learning Approach
Kalium Permanganat: Termodinamika Mengenai Transport Ionik dalam Air
Venue not supplied by source · 2018
Nur Intan Feronika, Rahadian Zainul
Read original paper ↗ ·a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement
Journal of Chemical Theory and Computation · 2019
Laura Pedraza‐González, Luca De Vico, Marı́a del Carmen Marı́n, Francesca Fanelli, Massimo Olivucci
Read original paper ↗ ·Enzymerhodopsins: novel photoregulated catalysts for optogenetics
Current Opinion in Structural Biology · 2019
Shatanik Mukherjee, Peter Hegemann, Matthias Broser
Read original paper ↗ ·Active Learning of Bayesian Linear Models with High-Dimensional Binary Features by Parameter Confidence-Region Estimation
Neural Computation · 2020
Yu Inatsu, Masayuki Karasuyama, Keiichi Inoue, Hideki Kandori, Ichiro Takeuchi
Read original paper ↗ ·RubyACRs, nonalgal anion channelrhodopsins with highly red-shifted absorption
Proceedings of the National Academy of Sciences · 2020
Elena G. Govorunova, Oleg A. Sineshchekov, Hai Li, Yumei Wang, Leonid S. Brown, John L. Spudich
Read original paper ↗ ·Active Learning for Level Set Estimation Under Input Uncertainty and Its Extensions
Neural Computation · 2020
Yu Inatsu, Masayuki Karasuyama, Keiichi Inoue, Ichiro Takeuchi
Read original paper ↗ ·On the Automatic Construction of QM/MM Models for Biological Photoreceptors: Rhodopsins as Model Systems
Challenges and advances in computational chemistry and physics · 2020
Laura Pedraza‐González, Marı́a del Carmen Marı́n, Luca De Vico, Xuchun Yang, Massimo Olivucci
Read original paper ↗ ·NeoR, a near-infrared absorbing rhodopsin
Nature Communications · 2020
Matthias Broser, Anika Spreen, Patrick E. Konold, Enrico Schiewer, Suliman Adam, Veniamin A. Borin, Igor Schapiro, Reinhard Seifert, John T. M. Kennis, Yinth Andrea Bernal Sierra, Peter Hegemann
Read original paper ↗ ·Insights into the Protein Functions and Absorption Wavelengths of Microbial Rhodopsins
The Journal of Physical Chemistry B · 2020
Masaki Tsujimura, Hiroshi Ishikita
Read original paper ↗ ·High Dimensional Level Set Estimation with Bayesian Neural Network
arXiv (Cornell University) · 2020
Huong Ha, Sunil Gupta, Santu Rana, Svetha Venkatesh
Read original paper ↗ ·Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins
Advances in experimental medicine and biology · 2021
Keiichi Inoue
Read original paper ↗ ·Sub-picosecond C = C bond photo-isomerization: evidence for the role of excited state mixing
Comptes Rendus Physique · 2021
Damianos Agathangelou, Partha Pratim Roy, Marı́a del Carmen Marı́n, Nicolas Ferré, Massimo Olivucci, Tiago Buckup, Jérémie Léonard, Stefan Haacke
Read original paper ↗ ·Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design
Communications Biology · 2021
Keiichi Inoue, Masayuki Karasuyama, Ryoko Nakamura, Masae Konno, Daichi Yamada, Kentaro Mannen, Takashi Nagata, Yu Inatsu, Hiromu Yawo, Kei Yura, Oded Béjà, Hideki Kandori, Ichiro Takeuchi
Read original paper ↗ ·Random Embeddings and Linear Regression can Predict Protein Function
arXiv (Cornell University) · 2021
Tianyu Lu, Alex Xijie Lu, Alan M Moses
Read original paper ↗ ·High Dimensional Level Set Estimation with Bayesian Neural Network
Proceedings of the AAAI Conference on Artificial Intelligence · 2021
Huong Ha, Sunil Gupta, Santu Rana, Svetha Venkatesh
Read original paper ↗ ·Evaluation of machine learning-based applications in forecasting the performance of single effect absorption chiller network
Thermal Science and Engineering Progress · 2021
Farshad Panahizadeh, Mahdi Hamzehei, Mahmood Farzaneh-Gord, Álvaro Antônio Ochoa Villa
Read original paper ↗ ·Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol
Topics in current chemistry collections · 2022
Laura Pedraza‐González, Leonardo Barneschi, Daniele Padula, Luca De Vico, Massimo Olivucci
Read original paper ↗ ·Far-Red Absorbing Rhodopsins, Insights From Heterodimeric Rhodopsin-Cyclases
Frontiers in Molecular Biosciences · 2022
Matthias Broser
Read original paper ↗ ·Mutational analyses identify a single amino acid critical for colour tuning in proteorhodopsins
FEBS Letters · 2022
Jin‐gon Shim, Na‐rae Kang, Kimleng Chuon, Shin‐Gyu Cho, Seanghun Meas, Kwang‐Hwan Jung
Read original paper ↗ ·Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol
Topics in Current Chemistry · 2022
Laura Pedraza‐González, Leonardo Barneschi, Daniele Padula, Luca De Vico, Massimo Olivucci
Read original paper ↗ ·Earliest Photic Zone Niches Probed by Ancestral Microbial Rhodopsins
Molecular Biology and Evolution · 2022
Cathryn D. Sephus, Evrim Fer, Amanda K. Garcia, Zachary R. Adam, Edward W. Schwieterman, Betül Kaçar
Read original paper ↗ ·Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering
Frontiers in Chemistry · 2022
Willem J. DeGrip, Srividya Ganapathy
Read original paper ↗ ·The binding of secondary chromophore for thermally stable rhodopsin makes more stable with temperature
Protein Science · 2022
Jin‐gon Shim, Kimleng Choun, Kun‐Wook Kang, Jihyun Kim, Shin‐Gyu Cho, Kwang‐Hwan Jung
Read original paper ↗ ·PhISCO: a simple method to infer phenotypes from protein sequences
bioRxiv (Cold Spring Harbor Laboratory) · 2022
Ayelen Sebastiana Hernandez Berthet, Ariel Alejandro Aptekmann, Jesús Tejero, Ignacio Enrique Sanchez, Martin Ezequiel Noguera, Ernesto A. Román
Read original paper ↗ ·Impact of protein–chromophore interaction on the retinal excited state and photocycle of Gloeobacter rhodopsin: role of conserved tryptophan residues
Chemical Science · 2023
Ramprasad Misra, Ishita R. Das, András Dér, Gábor Steinbach, Jin‐gon Shim, Wayne Busse, Kwang‐Hwan Jung, László Zimányi, Mordechai Sheves
Read original paper ↗ ·Induction effects on the absorption maxima of photoreceptor proteins
Biophysics and Physicobiology · 2023
Jonathan Richard Church, Jógvan Magnus Haugaard Olsen, Igor Schapiro
Read original paper ↗ ·Ion-pumping microbial rhodopsin protein classification by machine learning approach
BMC Bioinformatics · 2023
Muthu Krishnan Selvaraj, Anamika Thakur, Manoj Kumar, Anil Kumar Pinnaka, Chander Raman Suri, Siddhardha Busi, Senthil Prasad Elumalai
Read original paper ↗ ·Fine spectral tuning of a flavin-binding fluorescent protein for multicolor imaging
Journal of Biological Chemistry · 2023
Andrey Nikolaev, Anna Yudenko, Anastasia Smolentseva, Andrey O. Bogorodskiy, Fedor Tsybrov, Valentin I. Borshchevskiy, Siarhei M. Bukhalovich, Vera V. Nazarenko, Elizaveta Kuznetsova, Oleg Semenov, Alina Remeeva, Ivan Gushchin
Read original paper ↗ ·Optogenetic Methods in Plant Biology
Annual Review of Plant Biology · 2023
Kai Robert Konrad, Shiqiang Gao, Matias Daniel Zurbriggen, Georg Nagel
Read original paper ↗ ·Raman Optical Activity of Retinal Chromophore in Sensory Rhodopsin II
The Journal of Physical Chemistry B · 2023
Kouhei Nishikawa, Ryosuke Kuroiwa, Jun Tamogami, Masashi Unno, Tomotsumi Fujisawa
Read original paper ↗ ·Photochemistry of the Retinal Chromophore in Microbial Rhodopsins
The Journal of Physical Chemistry B · 2023
Keiichi Inoue
Read original paper ↗ ·Efficient model selection for predictive pattern mining model by safe pattern pruning
Patterns · 2023
Takumi Yoshida, Hiroyuki Hanada, Kazuya Nakagawa, Kouichi Taji, Koji Tsuda, Ichiro Takeuchi
Read original paper ↗ ·Opto-electronic feedback control of membrane potential for real-time control of action potentials
Cell Reports Methods · 2023
Balázs Ördög, Tim De Coster, S O Dekker, Cindy I. Bart, Juan Zhang, Gerard J.J. Boink, Wilhelmina H. Bax, Shanliang Deng, Bram L den Ouden, Antoine A.F. de Vries, Daniël A. Pijnappels
Read original paper ↗ ·Discovering genotype–phenotype relationships with machine learning and the Visual Physiology Opsin Database ( VPOD )
GigaScience · 2024
Seth A Frazer, Mahdi Baghbanzadeh, Ali Rahnavard, Keith A. Crandall, Todd H. Oakley
Read original paper ↗ ·Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins
Science Advances · 2024
Jiafei Mao, Xinsheng Jin, Man Shi, David J. Heidenreich, Lynda J. Brown, Richard C. D. Brown, Moreno Lelli, Xiao Dong He, Clemens Glaubitz
Read original paper ↗ ·Tetherless Optical Neuromodulation: Wavelength from Orange-red to Mid-infrared
Neuroscience Bulletin · 2024
Chao H. Sun, Qi Fan, Rou‐Gang Xie, Ceng Luo, Bingliang Hu, Quan Wang
Read original paper ↗ ·Associating protein sequence positions with the modulation of quantitative phenotypes
Archives of Biochemistry and Biophysics · 2024
Ayelen Sebastiana Hernandez Berthet, Ariel Alejandro Aptekmann, Jesús Tejero, Ignacio Enrique Sanchez, Martin Ezequiel Noguera, Ernesto A. Román
Read original paper ↗ ·Deep dive into the diversity and properties of rhodopsins in actinomycetes of the family Geodermatophilaceae
bioRxiv (Cold Spring Harbor Laboratory) · 2024
Sergey V. Tarlachkov, Irina P. Starodumova, Olga V. Boueva, Sergei V. Chernyshov, Lyudmila Ivanovna Evtushenko
Read original paper ↗ ·RhoMax: Computational Prediction of Rhodopsin Absorption Maxima Using Geometric Deep Learning
Journal of Chemical Information and Modeling · 2024
Meitar Sela, Jonathan Richard Church, Igor Schapiro, Dina Schneidman‐Duhovny
Read original paper ↗ ·Rhodopsin‐based light‐harvesting system for sustainable synthetic biology
Microbial Biotechnology · 2024
Weiming Tu, Haris Saeed, Wei E. Huang
Read original paper ↗ ·Sensing Light Underwater
Venue not supplied by source · 2024
Manuel Serif, Per Winge
Read original paper ↗ ·Reconstructing Early Microbial Life
Annual Review of Microbiology · 2024
Betül Kaçar
Read original paper ↗ ·Guest-Mediated Modulation of Photophysical Pathways in a Coronene Bisimide Cyclophane
Journal of the American Chemical Society · 2024
Jessica Rühe, Kavya Vinod, Hanna Hoh, Kazutaka Shoyama, Mahesh Hariharan, Frank Würthner
Read original paper ↗ ·Molecular Mechanisms Underlying the Spectral Shift in Zebrafish Cone Opsins
bioRxiv (Cold Spring Harbor Laboratory) · 2024
L. América Chi, Shubham Kumar Pandey, Wojciech Kołodziejczyk, Peik K. Lund-Andersen, Jonathan E. Barnes, Каріна Капуста, Jagdish Suresh Patel
Read original paper ↗ ·Structural changes of Natronomonas pharaonis halorhodopsin in its late photocycle revealed by solid-state NMR spectroscopy
Biophysical Chemistry · 2024
Xin Zhang, Hajime Tamaki, Takashi Kikukawa, Toshimichi Fujiwara, Yoh Matsuki
Read original paper ↗ ·Mode-Specific Photoresponse of Retinal Protonated Schiff Base Isomers in the Reversible Photochromic Reactions of Microbial and Animal Rhodopsins
The Journal of Physical Chemistry B · 2024
Pavel A. Kusochek, Olga A. Smitienko, Anastasia V. Bochenkova
Read original paper ↗ ·Deep dive into the diversity and properties of rhodopsins in actinomycetes of the family Geodermatophilaceae
Journal of Photochemistry and Photobiology B Biology · 2024
Sergey V. Tarlachkov, Irina P. Starodumova, Olga V. Boueva, Sergei V. Chernyshov, Lyudmila Ivanovna Evtushenko
Read original paper ↗ ·Origin of the red-shifted absorption maximum in channelrhodopsin Chrimson
Chemical Communications · 2025
Jonathan Richard Church, Probal Nag, Tal Dogon, Igor Schapiro
Read original paper ↗ ·Photofunctional cyclophane host–guest systems
Chemical Communications · 2025
Swadhin Garain, Frank Würthner
Read original paper ↗ ·Blue-shifted ancyromonad channelrhodopsins for multiplex optogenetics
eLife · 2025
Elena G. Govorunova, Oleg A. Sineshchekov, Hai Li, Yueyang Gou, Hongmei Chen, Shuyuan Yang, Yumei Wang, Stephen Mitchell, Alyssa Palmateer, Leonid S. Brown, François St-Pierre, Mingshan Xue, John L. Spudich
Read original paper ↗ ·