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Geometry Optimization Using the Frozen Domain and Partial Dimer Approaches in the Fragment Molecular Orbital Method: Implementation, Benchmark, and Applications to Protein Ligand-Binding Sites.
Okuwaki K, Watanabe N, Kato K, Watanabe C, Nakayama N, Kato A, Mochizuki Y, Nakano T, Honma T, Fukuzawa K. Okuwaki K, et al. Among authors: watanabe c. J Chem Inf Model. 2024 Dec 23;64(24):9449-9458. doi: 10.1021/acs.jcim.4c01280. Epub 2024 Dec 2. J Chem Inf Model. 2024. PMID: 39621552
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: watanabe h. 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
High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning.
Kato K, Masuda T, Watanabe C, Miyagawa N, Mizouchi H, Nagase S, Kamisaka K, Oshima K, Ono S, Ueda H, Tokuhisa A, Kanada R, Ohta M, Ikeguchi M, Okuno Y, Fukuzawa K, Honma T. Kato K, et al. Among authors: watanabe c. J Chem Inf Model. 2020 Jul 27;60(7):3361-3368. doi: 10.1021/acs.jcim.0c00273. Epub 2020 Jun 30. J Chem Inf Model. 2020. PMID: 32496771
FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method.
Takaya D, Watanabe C, Nagase S, Kamisaka K, Okiyama Y, Moriwaki H, Yuki H, Sato T, Kurita N, Yagi Y, Takagi T, Kawashita N, Takaba K, Ozawa T, Takimoto-Kamimura M, Tanaka S, Fukuzawa K, Honma T. Takaya D, et al. Among authors: watanabe c. J Chem Inf Model. 2021 Feb 22;61(2):777-794. doi: 10.1021/acs.jcim.0c01062. Epub 2021 Jan 29. J Chem Inf Model. 2021. PMID: 33511845
Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins.
Fukuzawa K, Kato K, Watanabe C, Kawashima Y, Handa Y, Yamamoto A, Watanabe K, Ohyama T, Kamisaka K, Takaya D, Honma T. Fukuzawa K, et al. Among authors: watanabe c, watanabe k. J Chem Inf Model. 2021 Sep 27;61(9):4594-4612. doi: 10.1021/acs.jcim.1c00694. Epub 2021 Sep 10. J Chem Inf Model. 2021. PMID: 34506132
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: watanabe c, watanabe h. 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.
974 results