@article{a907cd1f61934d299765159f3db57b4c,
title = "Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation",
abstract = "A combination of classical molecular dynamics (MD) simulation and ab initio fragment molecular orbital (FMO) calculation was applied to a complex formed between the main protease of the new coronavirus and the inhibitor N3 to calculate interactions within the complex while incorporating structural fluctuations mimicking physiological conditions. Namely, a statistical evaluation of interaction energies between N3 and amino acid residues was performed by processing a thousand of structure samples. It was found that relative importance of each residue is altered by the structural fluctuation. The MD-FMO combination should be promising to simulate protein related systems in a more realistic way.",
author = "Ryo Hatada and Koji Okuwaki and Kazuki Akisawa and Yuji Mochizuki and Yuma Handa and Kaori Fukuzawa and Yuto Komeiji and Yoshio Okiyama and Shigenori Tanaka",
note = "Funding Information: Acknowledgments For FMO calculations with ABINIT-MP, computational resources of the supercomputer Fugaku (the evaluation environment in the trial phase) were provided by the RIKEN Center for Computational Science (R-CCS) under a special project against COVID-19. Technical supports on Fugaku were provided by Drs. Kota Sakakura (FOCUS) and Hiromasa Watanabe (HPC Systems Inc.). All MD simulations were performed on TSUBAME3.0 at Tokyo Institute of Technology under a funding by AMED/BINDS (JP20am0101113). The present work was supported also by Rikkyo SFR as well as JSPS Kakenhi (JP17H06353, JP18K03825, and JP19K12010). ORCID iDs Koji Okuwaki https://orcid.org/0000-0002-4510-5717 Yuji Mochizuki https://orcid.org/0000-0002-7310-5183 Kaori Fukuzawa https://orcid.org/0000-0001-5357-8250 Yuto Komeiji https://orcid.org/0000-0002-9708- 6175 Yoshio Okiyama https://orcid.org/0000-0002-6775-8604 Shigenori Tanaka https://orcid.org/0000-0002-6659-2788 Funding Information: For FMO calculations with ABINIT-MP, computational resources of the supercomputer Fugaku (the evaluation environment in the trial phase) were provided by the RIKEN Center for Computational Science (R-CCS) under a special project against COVID-19. Technical supports on Fugaku were provided by Drs. Kota Sakakura (FOCUS) and Hiromasa Watanabe (HPC Systems Inc.). All MD simulations were performed on TSUBAME3.0 at Tokyo Institute of Technology under a funding by AMED/BINDS (JP20am0101113). The present work was supported also by Rikkyo SFR as well as JSPS Kakenhi (JP17H06353, JP18K03825, and JP19K12010). Publisher Copyright: {\textcopyright} 2021 The Japan Society of Applied Physics",
year = "2021",
month = feb,
doi = "10.35848/1882-0786/abdac6",
language = "English",
volume = "14",
journal = "Applied Physics Express",
issn = "1882-0778",
publisher = "Japan Society of Applied Physics",
number = "2",
}