Ab initio quantum mechanical study of the binding energies of human estrogen receptor with its ligands: An application of fragment molecular orbital method. - Kaori Fukuzawa; Kazuo Kitaura; Masami Uebayasi; Kotoko Nakata; Tsuguchika Kaminuma; Tatsuya Nakano (J. Comput. Chem., 2005)

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study. - Kaori Fukuzawa; Yuto Komeiji; Yuji Mochizuki; Akifumi Kato; Tatsuya Nakano; Shigenori Tanaka (J. Comput. Chem., 2006)

VISCANA: Visualized Cluster Analysis of Protein-Ligand Interaction Based on the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening. - Shinji Amari; Masahiro Aizawa; Junwei Zhang; Kaori Fukuzawa; Yuji Mochizuki; Yoshio Iwasawa; Kotoko Nakata; Hiroshi Chuman; Tatsuya Nakano (J. Chem. Inf. Model., 2006)

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study. - Kaori Fukuzawa; Yuto Komeiji; Yuji Mochizuki; Akifumi Kato; Tatsuya Nakano; Shigenori Tanaka (J. Comput. Chem., 2007)

Theoretical analysis of binding specificity of influenza viral hemagglutinin to avian and human receptors based on the fragment molecular orbital method. - Tatsunori Iwata; Kaori Fukuzawa; Katsuhisa Nakajima; Sachiko Aida-Hyugaji; Yuji Mochizuki; Hirofumi Watanabe; Shigenori Tanaka (Comput. Biol. Chem., 2008)

Water-mediated interactions in the CRP-cAMP-DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site? - Bryan M. B. VanSchouwen; Heather L. Gordon; Stuart M. Rothstein; Yuto Komeiji; Kaori Fukuzawa; Shigenori Tanaka (Comput. Biol. Chem., 2008)

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. - Chiduru Watanabe; Hirofumi Watanabe; Kaori Fukuzawa; Lorien J. Parker; Yoshio Okiyama; Hitomi Yuki; Shigeyuki Yokoyama; Hirofumi Nakano; Shigenori Tanaka; Teruki Honma (J. Chem. Inf. Model., 2017)

Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations. - Takaki Tokiwa; Shogo Nakano; Yuta Yamamoto; Takeshi Ishikawa; Sohei Ito; Vladimír Sládek; Kaori Fukuzawa; Yuji Mochizuki; Hiroaki Tokiwa; Fuminori Misaizu; Yasuteru Shigeta (J. Chem. Inf. Model., 2019)

Fragmentation at sp2 carbon atoms in fragment molecular orbital method. - Yoshinobu Akinaga; Koichiro Kato; Tatsuya Nakano; Kaori Fukuzawa; Yuji Mochizuki (J. Comput. Chem., 2020)

Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID: 6LU7). - Ryo Hatada; Koji Okuwaki; Yuji Mochizuki; Yuma Handa; Kaori Fukuzawa; Yuto Komeiji; Yoshio Okiyama; Shigenori Tanaka (J. Chem. Inf. Model., 2020)

High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning. - Koichiro Kato; Tomohide Masuda; Chiduru Watanabe; Naoki Miyagawa; Hideo Mizouchi; Shumpei Nagase; Kikuko Kamisaka; Kanji Oshima; Satoshi Ono; Hiroshi Ueda; Atsushi Tokuhisa; Ryo Kanada; et al. (J. Chem. Inf. Model., 2020)

Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins. - Kaori Fukuzawa; Koichiro Kato; Chiduru Watanabe; Yusuke Kawashima; Yuma Handa; Ami Yamamoto; Kazuki Watanabe 005; Tatsuya Ohyama; Kikuko Kamisaka; Daisuke Takaya; Teruki Honma (J. Chem. Inf. Model., 2021)

FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method. - Daisuke Takaya; Chiduru Watanabe; Shunpei Nagase; Kikuko Kamisaka; Yoshio Okiyama; Hirotomo Moriwaki; Hitomi Yuki; Tomohiro Sato; Noriyuki Kurita; Yoichiro Yagi; Tatsuya Takagi; Norihito Kawashita; et al. (J. Chem. Inf. Model., 2021)

Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy. - Kenichiro Takaba; Chiduru Watanabe; Atsushi Tokuhisa; Yoshinobu Akinaga; Biao Ma; Ryo Kanada; Mitsugu Araki; Yasushi Okuno; Yusuke Kawashima; Hirotomo Moriwaki; Norihito Kawashita; Teruki Honma; et al. (J. Comput. Chem., 2022)

Structural and Computational Analyses of the Unique Interactions of Opicapone in the Binding Pocket of Catechol O-Methyltransferase: A Crystallographic Study and Fragment Molecular Orbital Analyses. - Katsuki Takebe; Mamoru Suzuki; Takao Kuwada-Kusunose; Satoko Shirai; Kaori Fukuzawa; Tomoko Takamiya; Narikazu Uzawa; Hiroshi Iijima (J. Chem. Inf. Model., 2023)

FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses. - Hirotomo Moriwaki; Yusuke Kawashima; Chiduru Watanabe; Kikuko Kamisaka; Yoshio Okiyama; Kaori Fukuzawa; Teruki Honma (J. Chem. Inf. Model., 2024)

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. - Koji Okuwaki; Naoki Watanabe; Koichiro Kato; Chiduru Watanabe; Naofumi Nakayama; Akifumi Kato; Yuji Mochizuki; Tatsuya Nakano; Teruki Honma; Kaori Fukuzawa (J. Chem. Inf. Model., 2024)