Okiyama Y - Search Results

1

Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design.

Watanabe C, Fukuzawa K, Okiyama Y, Tsukamoto T, Kato A, Tanaka S, Mochizuki Y, Nakano T. Watanabe C, et al. Among authors: okiyama y. J Mol Graph Model. 2013 Apr;41:31-42. doi: 10.1016/j.jmgm.2013.01.006. Epub 2013 Feb 8. J Mol Graph Model. 2013. PMID: 23467020

2

Prediction of probable mutations in influenza virus hemagglutinin protein based on large-scale ab initio fragment molecular orbital calculations.

Yoshioka A, Fukuzawa K, Mochizuki Y, Yamashita K, Nakano T, Okiyama Y, Nobusawa E, Nakajima K, Tanaka S. Yoshioka A, et al. Among authors: okiyama y. J Mol Graph Model. 2011 Sep;30:110-9. doi: 10.1016/j.jmgm.2011.06.011. Epub 2011 Jul 6. J Mol Graph Model. 2011. PMID: 21798776

3

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.

Tanaka S, Mochizuki Y, Komeiji Y, Okiyama Y, Fukuzawa K. Tanaka S, et al. Among authors: okiyama y. Phys Chem Chem Phys. 2014 Jun 14;16(22):10310-44. doi: 10.1039/c4cp00316k. Phys Chem Chem Phys. 2014. PMID: 24740821 Review.

4

Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method.

Tokuda K, Watanabe C, Okiyama Y, Mochizuki Y, Fukuzawa K, Komeiji Y. Tokuda K, et al. Among authors: okiyama y. J Mol Graph Model. 2016 Sep;69:144-53. doi: 10.1016/j.jmgm.2016.08.004. Epub 2016 Aug 31. J Mol Graph Model. 2016. PMID: 27611645

5

Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach.

Watanabe C, Watanabe H, Fukuzawa K, Parker LJ, Okiyama Y, Yuki H, Yokoyama S, Nakano H, Tanaka S, Honma T. Watanabe C, et al. Among authors: okiyama y. J Chem Inf Model. 2017 Dec 26;57(12):2996-3010. doi: 10.1021/acs.jcim.7b00110. Epub 2017 Dec 1. J Chem Inf Model. 2017. PMID: 29111719

6

Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: Implementation and DNA Study.

Okiyama Y, Nakano T, Watanabe C, Fukuzawa K, Mochizuki Y, Tanaka S. Okiyama Y, et al. J Phys Chem B. 2018 Apr 26;122(16):4457-4471. doi: 10.1021/acs.jpcb.8b01172. Epub 2018 Apr 16. J Phys Chem B. 2018. PMID: 29558137

7

Towards good correlation between fragment molecular orbital interaction energies and experimental IC₅₀ for ligand binding: A case study of p38 MAP kinase.

Sheng Y, Watanabe H, Maruyama K, Watanabe C, Okiyama Y, Honma T, Fukuzawa K, Tanaka S. Sheng Y, et al. Among authors: okiyama y. Comput Struct Biotechnol J. 2018 Oct 13;16:421-434. doi: 10.1016/j.csbj.2018.10.003. eCollection 2018. Comput Struct Biotechnol J. 2018. PMID: 30450166 Free PMC article.

8

Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies.

Okiyama Y, Watanabe C, Fukuzawa K, Mochizuki Y, Nakano T, Tanaka S. Okiyama Y, et al. J Phys Chem B. 2019 Feb 7;123(5):957-973. doi: 10.1021/acs.jpcb.8b09326. Epub 2018 Dec 28. J Phys Chem B. 2019. PMID: 30532968

9

Taking Water into Account with the Fragment Molecular Orbital Method.

Okiyama Y, Fukuzawa K, Komeiji Y, Tanaka S. Okiyama Y, et al. Methods Mol Biol. 2020;2114:105-122. doi: 10.1007/978-1-0716-0282-9_7. Methods Mol Biol. 2020. PMID: 32016889 Review.

10

Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID: 6LU7).

Hatada R, Okuwaki K, Mochizuki Y, Handa Y, Fukuzawa K, Komeiji Y, Okiyama Y, Tanaka S. Hatada R, et al. Among authors: okiyama y. J Chem Inf Model. 2020 Jul 27;60(7):3593-3602. doi: 10.1021/acs.jcim.0c00283. Epub 2020 Jun 25. J Chem Inf Model. 2020. PMID: 32539372

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