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Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms

https://doi.org/10.1021/jacs.3c02229

Grigorenko, Bella L; Polyakov, Igor V; Khrenova, Maria G; Giudetti, Goran; Faraji, Shirin; Krylov, Anna I; Nemukhin, Alexander V (June 2023, Journal of the American Chemical Society)

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How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur

https://doi.org/10.1021/acs.jctc.2c00286

Giudetti, Goran; Polyakov, Igor; Grigorenko, Bella L.; Faraji, Shirin; Nemukhin, Alexander V.; Krylov, Anna I. (August 2022, Journal of Chemical Theory and Computation)

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Interplay between Locally Excited and Charge Transfer States Governs the Photoswitching Mechanism in the Fluorescent Protein Dreiklang

https://doi.org/10.1021/acs.jpcb.0c09221

Sen, Tirthendu; Ma, Yingying; Polyakov, Igor V.; Grigorenko, Bella L.; Nemukhin, Alexander V.; Krylov, Anna I. (January 2021, The Journal of Physical Chemistry B)
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Computational Modeling Reveals the Mechanism of Fluorescent State Recovery in the Reversibly Photoswitchable Protein Dreiklang

https://doi.org/10.1021/acs.jpcb.9b06988

Grigorenko, Bella L.; Polyakov, Igor V.; Krylov, Anna I.; Nemukhin, Alexander V. (September 2019, The Journal of Physical Chemistry B)

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Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes

https://doi.org/10.1021/acs.jpcb.9b00591

Nemukhin, Alexander V.; Grigorenko, Bella L.; Khrenova, Maria G.; Krylov, Anna I. (June 2019, The Journal of Physical Chemistry B)

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Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing?

https://doi.org/10.1021/acs.chemrev.6b00238

Acharya, Atanu; Bogdanov, Alexey M; Grigorenko, Bella L; Bravaya, Ksenia B; Nemukhin, Alexander V; Lukyanov, Konstantin A; Krylov, Anna I (January 2017, Chemical Reviews)

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Frontiers in Multiscale Modeling of Photoreceptor Proteins

https://doi.org/10.1111/php.13372

Mroginski, Maria‐Andrea; Adam, Suliman; Amoyal, Gil S.; Barnoy, Avishai; Bondar, Ana‐Nicoleta; Borin, Veniamin A.; Church, Jonathan R.; Domratcheva, Tatiana; Ensing, Bernd; Fanelli, Francesca; et al (February 2021, Photochemistry and Photobiology)

Abstract This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.
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