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)

Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation. - Yuto Komeiji; Takeshi Ishikawa; Yuji Mochizuki; Hiroshi Yamataka; Tatsuya Nakano (J. Comput. Chem., 2009)

Gröbner Basis Technique for Algebraic Formulas in Electron Correlation Theories. - Takeshi Osoekawa; Naoyuki Shinohara; Yuji Mochizuki; Kazuhiro Yokoyama (ICCSA Workshops, 2010)

Development of QC2AS - A Computer Algebra System for Symbolic Quantum Chemical Computations. - Takeshi Osoekawa; Yuji Mochizuki; Kazuhiro Yokoyama (ICCSA Workshops, 2011)

A privacy-preserving collaborative filtering protocol considering updates. - Yuji Mochizuki; Yoshifumi Manabe (APSITT, 2015)

RI-MP3 calculations of biomolecules based on the fragment molecular orbital method. - Takeshi Ishikawa; Kota Sakakura; Yuji Mochizuki (J. Comput. Chem., 2018)

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)

Size-consistency and orbital-invariance issues revealed by VQE-UCCSD calculations with the FMO scheme. - Kenji Sugisaki; Tatsuya Nakano; Yuji Mochizuki (J. Comput. Chem., 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)

Enhancement of energy decomposition analysis in fragment molecular orbital calculations. - Sota Matsuoka; Kota Sakakura; Yoshinobu Akinaga; Kazuki Akisawa; Koji Okuwaki; Hideo Doi; Yuji Mochizuki (J. Comput. Chem., 2024)

Large-Scale FMO-MP2 Calculations of the Spike Protein Droplet Model. - Hideo Doi; Tatsuya Nakano; Kota Sakakura; Kazuki Akisawa; Koji Okuwaki; Yoshinori Hirano; Eiji Yamamoto; Kenji Yasuoka; Satoshi Ohshima; Takahiro Katagiri; Yuji Mochizuki (J. Comput. Chem., 2025)