-
Geometry Optimization using the Frozen Domain and Partial Dimer Approach with the Fragment Molecular Orbital Method: Implementation, Benchmark, and Application for Ligand-Binding Site of Proteins
Koji Okuwaki, Naoki Watanabe, Koichiro Kato, Chiduru Watanabe, Naofumi Nakayama, Akifumi Kato, Yuji Mochizuki, Tatsuya Nakano, Teruki Honma, Kaori Fukuzawa
24 7 2024
-
DPD simulation to reproduce lipid membrane microdomains based on fragment molecular orbital calculations
Peer-reviewed
Hideo Doi, Yushi Osada, Yusuke Tachino, Koji Okuwaki, Melvin Wei Shern Goh, Ryugo Tero, Yuji Mochizuki
Applied Physics Express17
055001
5 2024
-
Size-consistency and orbital-invariance issues revealed by VQE-UCCSD calculations with the FMO scheme
Peer-reviewed
International journal
Kenji Sugisaki, Tatsuya Nakano, Yuji Mochizuki
J. Comp. Chem.45
2204
-
2213
5 2024
-
Prediction of Binding Pose and Affinity of Nelfinavir, a SARS-CoV-2 Main Protease Repositioned Drug, by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations
Peer-reviewed
International journal
Yuma Handa, Koji Okuwaki, Yusuke Kawashima, Ryo Hatada, Yuji Mochizuki, Yuto Komeiji, Shigenori Tanaka, Takayuki Furuishi, Etsuo Yonemochi, Teruki Honma, Kaori Fukuzawa
The Journal of Physical Chemistry B128
(
10
)
2249
-
2265
4 3 2024
-
Towards tailoring hydrophobic interaction with uranyl(VI) oxygen for C-H activation
Peer-reviewed
International journal
Satoru Tsushima, Jérôme Kretzschmar, Hideo Doi, Koji Okuwaki, Masashi Kaneko, Yuji Mochizuki, Koichiro Takao
Chem. Comm.60
4769
-
4772
3 2024
-
Enhancement of energy decomposition analysis in fragment molecular orbital calculations
Peer-reviewed
International journal
Sota Matsuoka, Kota Sakakura, Yoshinobu Akinaga, Kazuki Akisawa, Koji Okuwaki, Hideo Doi, Yuji Mochizuki
J. Comp. Chem.45
898
-
902
3 2024
-
Development of reverse mapping system bridging dissipative particle dynamics and fragment molecular orbital calculation
Peer-reviewed
Koji Okuwaki, Hideo Doi, Taku Ozawa, Yuji Mochizuki
Japanese Journal of Applied Physics62
(
11
)
110902
23 10 2023
-
Bayesian phase difference estimation algorithm for direct calculation of fine structure splitting: accelerated simulation of relativistic and quantum many-body effects
Peer-reviewed
Kenji Sugisaki, Srinivasa Prasannaa, Satoshi Ohshima, Takahiro Katagiri, Yuji Mochizuki, Bijaya Kumar Sahoo, Bhanu Pratap Das
Electronic Structure5
(
3
)
035006
12 9 2023
-
Dissipative particle dynamics simulation for peptoid nanosheet with non-empirical parameter set
Peer-reviewed
Yusuke Tachino, Koji Okuwaki, Hideo Doi, Kazuki Akisawa, Yuji Mochizuki
Japanese Journal of Applied Physics62
(
9
)
090902
23 8 2023
-
Machine learning to improve efficiency of non-empirical interaction parameter for dissipative particle dynamics (DPD) simulation
Peer-reviewed
Hideo Doi, Sota Matsuoka, Koji Okuwaki, Ryo Hatada, Soujiro Minami, Ryosuke Suhara, Yuji Mochizuki
Japanese Journal of Applied Physics62
(
7
)
070901
7 7 2023
-
Bifurcated Hydrogen Bonds in a Peptide Crystal Unveiled by X-ray Diffraction and Polarized Raman Spectroscopy
Peer-reviewed
Kazunori Motai, Nao Koishihara, Takuma Narimatsu, Hiroyoshi Ohtsu, Masaki Kawano, Yuki Wada, Kazuki Akisawa, Koji Okuwaki, Takehiko Mori, Ji-Seon Kim, Yuji Mochizuki, Yuhei Hayamizu
Crystal Growth & Design23
(
6
)
4556
-
4561
10 5 2023
-
Practical Computational Chemistry Course for a Comprehensive Understanding of Organic, Inorganic, and Physical Chemistry: From Molecular Interactions to Chemical Reactions
Peer-reviewed
International journal
Nahoko Kuroki, Yuji Mochizuki, Hirotoshi Mori
J. Chem. Educ.100
(
2
)
647
-
654
4 1 2023
-
Lattice Folding Simulation of Peptide by Quantum Computation
Peer-reviewed
Rui SAITO, Koji OKUWAKI, Yuji MOCHIZUKI, Ryutaro NAGAI, Takumi KATO, Kenji SUGISAKI, Yuichiro MINATO
Journal of Computer Chemistry, Japan -International Edition9
(
2022
)
2036
2023
-
Variational quantum eigensolver simulations with the multireference unitary coupled cluster ansatz: a case study of the C2v quasi-reaction pathway of beryllium insertion into a H2 molecule
Peer-reviewed
International journal
Kenji Sugisaki, Takumi Kato, Yuichiro Minato, Koji Okuwaki, Yuji Mochizuki
Phys. Chem. Chem. Phys.24
8439
-
8452
15 3 2022
-
Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method
Peer-reviewed
K. Okuwaki, K. Akisawa, R. Hatada, Y. Mochizuki, K. Fukuzawa, Y. Komeiji, S. Tanaka
Applied Physics Express15
017001
24 12 2021
-
Interaction Analysis on the SARS-CoV-2 Spike Protein Receptor Binding Domain Using Visualization of the Interfacial Electrostatic Complementarity
Peer-reviewed
Takeshi Ishikawa, Hiroki Ozono, Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Yuji Mochizuki
J. Phys. Chem. Lett.12
11267
-
11272
12 11 2021
-
Fragment Molecular Orbital Based Interaction Analyses on Complexes Between SARS-CoV-2 RBD Variants and ACE2
Peer-reviewed
Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Shun Kitahara, Yusuke Tachino, Yuji Mochizuki, Yuto Komeiji, Shigenori Tanaka
Jpn. J. Appl. Phys.60
(
9
)
090901
13 8 2021
-
Dynamical Cooperativity of Ligand-Residue Interactions Evaluated with the Fragment Molecular Orbital Method
Peer-reviewed
Shigenori Tanaka, Shusuke Tokutomi, Ryo Hatada,, Koji Okuwaki, Kazuki Akisawa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki
J. Phys. Chem. B125
(
24
)
6501
-
6512
14 6 2021
-
Density-Matrix Based Scheme of Basis Selection for Linear Combination of Fragment Molecular Orbitals
Peer-reviewed
International journal
Yoshio Okiyama, Yuji Mochizuki, Masanori Yamanaka, Shigenori Tanaka
J. Phys. Soc. Jpn.90
(
6
)
064301
-
064301
5 2021
-
分子動力学計算とFMO計算を用いたSARS-CoV-2メインプロテアーゼと既存薬との結合性予測
半田 佑磨, 川嶋 裕介, 畑田 崚, 奥脇 弘次, 望月 祐志, 古明地 勇人, 田中 成典, 本間 光貴, 古石 誉之, 福澤 薫, 米持 悦生
日本薬学会年会要旨集141年会
27V04
-
am12S
3 2021
-
Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations
Peer-reviewed
International journal
Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka
RSC Advances11
(
6
)
3272
-
3279
14 1 2021
-
Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation
Peer-reviewed
Ryo Hatada, Koji Okuwaki, Kazuki Akisawa, Yuji Mochizuki, Yuma Handa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka
Applied Physics Express14
027003
1 2021
-
Extension to Multiscale Simulations
Invited
Koji Okuwaki, Taku Ozawa, Yuji Mochizuki
Recent Advances of the Fragment Molecular Orbital Method
529
-
546
1 2021
-
Modeling of Solid and Surface
Koichiro Kato, Aya Hashimoto, Eiichi Tamiya, Kaori Fukuzawa, Yuichiro Ishikawa, Yuji Mochizuki
Recent Advances of the Fragment Molecular Orbital Method
407
-
424
1 2021
-
The ABINIT-MP Program
Invited
Yuji Mochizuki, Tatsuya Nakano, Kota Sakakura, Yoshio Okiyama, Hiromasa Watanabe, Koichiro Kato, Yoshinobu Akinaga, Shinya Sato, Jun-inchi Yamamoto, Katsumi Yamashita, Tadashi Murase, Takeshi Ishikawa, Yuto Komeiji, Yuji Kato, Naoki Watanabe, Takashi Tsukamoto, Hirotoshi Mori, Koji Okuwaki, Shigenori Tanaka, Akifumi Kato, Chiduru Watanabe, Kaori Fukuzawa
Recent Advances of the Fragment Molecular Orbital Method
53
-
67
1 2021
-
Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital (FMO) Method
Peer-reviewed
Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuto Komeiji, Katsunori Segawa, Yuji Mochizuki
Bull. Chem. Soc. Jpn.94
(
1
)
91
-
96
1 2021
-
Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID: 6LU7).
Peer-reviewed
International journal
Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Yuma Handa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka
Journal of chemical information and modeling60
(
7
)
3593
-
3602
25 6 2020
-
Self-Degradable Lipid-Like Materials Based on "Hydrolysis accelerated by the intra-Particle Enrichment of Reactant (HyPER)" for Messenger RNA Delivery
Peer-reviewed
Hiroki Tanaka, Tatsunari Takahashi, Manami Konishi, Nae Takata, Masaki Gomi, Daiki Shirane, Ryo Miyama, Shinya Hagiwara, Yuki Yamasaki, Yu Sakurai, Keisuke Ueda, Kenjirou Higashi, Kunikazu Moribe, Eiji Shinsho, Ruka Nishida, Kaori Fukuzawa, Etsuo Yonemochi, Koji Okuwaki, Yuji Mochizuki, Yuta Nakai, Kota Tange, Hiroki Yoshioka, Shinya Tamagawa, Hidetaka Akita
ADVANCED FUNCTIONAL MATERIALS30
(
34
)
1910575-1
-
1910575-17
6 2020
-
小角X線散乱と分子シミュレーションを融合したDOPC/Cholesterol二重膜の物性解析
新庄 永治, 西田 瑠花, 奥脇 弘次, 望月 祐志, 古石 誉之, 福澤 薫, 米持 悦生
日本薬学会年会要旨集140年会
27Y
-
pm04S
3 2020
-
Fragmentation at sp2 carbon in fragment molecular orbital (FMO) method
Peer-reviewed
Yoshinobu Akinaga, Kouichiro Kato, Tatsuya Nakano, Kaori Fukuzawa, Yuji Mochizuki
J. Comp. Chem.41
1416
-
1420
3 2020
-
Ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) simulations of (NH3)32 cluster: effects of electron correlation
Peer-reviewed
Moeko Ninomiya, Hideo Doi, Yoshiteru Matsumoto, Yuji Mochizuki, Yuto Komeiji
Bulletin of the Chemical Society of Japan93
(
4
)
553
-
560
2 2020
-
Interaction Analyses between Calcite/Apatite and Peptides by Fragment Molecular Orbital Method
Peer-reviewed
Ryo HATADA, Kouichiro KATO, Koji OKUWAKI, Kaori FUKUZAWA, Yuji MOCHIZUKI
Journal of Computer Chemistry, Japan19
(
1
)
1
-
7
2020
-
Stabilization Mechanism for a Nonfibrillar Amyloid β Oligomer Based on Formation of a Hydrophobic Core Determined by Dissipative Particle Dynamics
Peer-reviewed
Ryoko Kawai, Shuntaro Chiba, Koji Okuwaki, Ryo Kanada, Hideo Doi, Masahiro Ono, Yuji Mochizuki, Yasushi Okuno
ACS Chemical Neuroscience20
(
11
)
385
-
394
1 2020
-
Folding simulation of small proteins by dissipative particle dynamics (DPD) with non-empirical interaction parameters based on fragment molecular orbital calculations
Peer-reviewed
Koji Okuwaki, Hideo Doi, Kaori Fukuzawa, Yuji Mochizuki
Applied Physics Express13
017002
1 2020
-
Interaction between calcite and adsorptive peptide analyzed by fragment molecular orbital method
Peer-reviewed
Koichiro Kato, Kaori Fukuzawa, Yuji Mochizuki
Japanese Journal of Applied Physics58
(
12
)
120906
-
120906
1 12 2019
-
Reduction of Orbital Space for Molecular Orbital Calculations with Quantum Computation Simulator for Educations
Yuji Mochizuki Koji Okuwaki Takumi Kato Yuichiro Minato
ChemRxiv
9 2019
-
Cm3+/Eu3+ induced structural, mechanistic and functional implications for calmodulin
Peer-reviewed
Björn Drobot, Moritz Schmidt, Yuji Mochizuki, Takaya Abe, Koji Okuwaki, Florian Brulfert, Sven Falke, Sergey A. Samsonov, Yuto Komeiji, Christian Betzel, Thorsten Stumpf, Johannes Raff, Satoru Tsushima
Phys. Chem. Chem. Phys.21
(
38
)
21213
-
21222
8 2019
-
物性測定とFMO-DPD法による脂質微粒子の構造解析
Peer-reviewed
新庄 永治, 奥脇 弘次, 土居 英男, 望月 祐志, 古石 誉之, 福澤 薫, 米持 悦生
日本DDS学会学術集会プログラム予稿集35回
135
-
135
6 2019
-
小角X線散乱測定とFMO-DPDシミュレーションによる脂質/Cholesterol混合二重膜における物性の解析
Peer-reviewed
新庄 永治, 奥脇 弘次, 土居 英男, 望月 祐志, 古石 誉之, 福澤 薫, 米持 悦生
日本薬学会年会要旨集139年会
(
4
)
80
-
80
3 2019
-
Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies
Peer-reviewed
Yoshio Okiyama, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka
The Journal of Physical Chemistry B123
(
5
)
957
-
973
7 2 2019
-
Destabilization of DNA through interstrand crosslinking by UO22+
Peer-reviewed
Andr{\'{e } } Rossberg, Takaya Abe, Koji Okuwaki, Astrid Barkleit, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Satoru Tsushima
Chemical Communications55
(
14
)
2015
-
2018
2 2019
-
X線小角散乱と散逸粒子動力学法を用いた脂質膜およびベシクル形成メカニズムの解明
Peer-reviewed
新庄永治, 奥脇弘次, 土居英男, 望月祐志, 古石誉之, 福澤薫, 米持悦生
J. Comp. Chem. Jpn.17
(
4
)
172
-
179
1 2019
-
A Radical Correction for Inter Fragment Interaction Energy (IFIE) between Fragments Sharing Bond Detached Atom (BDA)
Peer-reviewed
Tatsuya Nakano, Yuji Mochidzuki, Kaori Fukuzawa, Yoshio Okiyama, Chiduru Watanabe
Journal of Computer Aided Chemistry20
(
0
)
1
-
6
2019
-
Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations
Peer-reviewed
Takaki Tokiwa, Shogo Nakano, Yuta Yamamoto, Takeshi Ishikawa, Sohei Ito, Vladimir Sladek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu, Yasuteru Shigeta
Journal of Chemical Information and Modeling59
(
1
)
25
-
30
1 2019
-
Deeper Level Parallelization and Performance Evaluation ofFMO Program ABINIT-MP on Oakforest-PACS
Invited
Peer-reviewed
MOCHIZUKI Yuji
J. Comp. Chem. Jpn.17
147
-
149
11 2018
-
Interaction between a Single-Stranded DNA and a Binding Protein Viewed by the Fragment Molecular Orbital Method
Peer-reviewed
Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa
Bulletin of the Chemical Society of Japan91
(
11
)
1596
-
1605
11 2018
-
<b>Accuracy of Dimer-ES Approximation on Fragment Molecular Orbital (FMO) Method</b><b> </b>
Peer-reviewed
Tatsuya Nakano, Kaori Fukuzawa, Yoshio Okiyama, Chiduru Watanabe, Yuto Komeiji, Yuji Mochizuki
Chem-Bio Informatics Journal18
(
0
)
119
-
122
5 10 2018
-
Theoretical Analyses on Water Cluster Structures in Polymer Electrolyte Membrane by Using Dissipative Particle Dynamics Simulations with Fragment Molecular Orbital Based Effective Parameters
Peer-reviewed
Okuwaki Koji, Mochizuki Yuji, Doi Hideo, Kawada Shutaro, Ozawa Taku, Yasuoka Kenji
RSC Advances8
(
60
)
34582
-
34595
10 2018
-
RI-MP3 calculations of biomolecules based on the fragment molecular orbital method
Peer-reviewed
Journal of Computer Chemistry, Japan39
1970
-
1978
9 2018
-
AIを活用した流体解析シミュレーション技術の開発
小杉範仁, 近藤修司, 秋永宜伸, 望月祐志
機械設計62
42
-
46
7 2018
-
A portable code for dissipative particle dynamics (DPD) simulations with additional specific interactions
Peer-reviewed
Okuwaki Koji, Naito Takamitsu, Saitou Sona, Mochizuki Yuji, other
Chem-Bio Informatics Journal
6 2018
-
Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study
Peer-reviewed
Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka
The Journal of Physical Chemistry B122
(
16
)
4457
-
4471
26 4 2018
-
Development of the Fragment Molecular Orbital Method for Calculating Nonlocal Excitations in Large Molecular Systems
Peer-reviewed
Takatoshi Fujita, Yuji Mochizuki
Journal of Physical Chemistry A122
(
15
)
3886
-
3898
19 4 2018
-
Development and Performance Evaluation of a Simulation Code for Dissipative Particle Dynamics (DPD) CAMUS
Peer-reviewed
Doi Hideo, Saitou Sona, Okuwaki Koji, Naito Takamitsu, Mochizuki Yuji
Journal of Computer Chemistry, Japan16
(
5
)
126
2 2018
-
An automated framework to evaluate effective interactionparameters for dissipative particle dynamics simulations basedon the fragment molecular orbital (FMO) method
Peer-reviewed
Okuwaki Koji, Doi Hideo, Mochizuki Yuji
Journal of Computer Chemistry, Japan17
(
2
)
102
2 2018
-
Fragment Molecular Orbital Based Parametrization Procedure for Mesoscopic Structure Prediction of Polymeric Materials
Peer-reviewed
Koji Okuwaki, Yuji Mochizuki, Hideo Doi, Taku Ozawa
Journal of Physical Chemistry B122
(
1
)
338
-
347
11 1 2018
-
FMO計算-粗視化シミュレーション連携手法の開発と応用
Peer-reviewed
奥脇弘次, 土居英男, 望月祐志, 小沢拓, 泰岡顕治, 福澤薫
J. Comp. Chem. Jpn.17
144
-
146
2018
-
大学初年度向け化学教育のためのScratchプログラムの開発
Peer-reviewed
満野仁美, 中川知樹, 土居英男, 望月祐志
J. Comp. Chem. Jpn.17
111
-
112
2018
-
フラグメント分子軌道(FMO)法を用いた散逸粒子動力学シミュレーションのための有効相互作用パラメータ算出の自動化フレームワーク
Peer-reviewed
奥脇弘次, 土居英男, 望月祐志
J. Comp. Chem. Jpn.17
102
-
109
2018
-
Application of tensorflow to recognition of visualized results of fragment molecular orbital (FMO) calculations
Peer-reviewed
Sona Saitou, Jun Iijima, Mayu Fujimoto, Yuji Mochizuki, Koji Okuwaki, Hideo Doi, Yuto Komeiji
Chem-Bio Informatics Journal18
58
-
69
1 1 2018
-
Development and Application of FMO Calculation − DPD Simulation Conbination Scheme
Peer-reviewed
Okuwaki Koji, Doi Hideo, Mochizuki Yuji, Ozawa Taku, Yasuoka Kenji, Fukuzawa Kaori
Journal of Computer Chemistry, Japan17
(
3
)
144
2018
-
Formation Mechanism of Lipid Membrane and Vesicle Using Small Angle X-ray Scattering and Dissipative Particle Dynamics (DPD) Method
Peer-reviewed
Eiji Shinsho, Koji Okuwaki, Hideo Doi, Yuji Mochizuki, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi
JOURNAL OF COMPUTER CHEMISTRY-JAPAN17
(
4
)
172
-
179
2018
-
Dissipative particle dynamics (DPD) simulations with fragment molecular orbital (FMO) based effective parameters for 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) membrane
Peer-reviewed
Hideo Doi, Koji Okuwaki, Yuji Mochizuki, Taku Ozawa, Kenji Yasuoka
CHEMICAL PHYSICS LETTERS684
427
-
432
9 2017
-
Theoretical Calculations on Cation-capturing ofMacrocyclic Peptoid with Phenyl Rings in Main Chain
Peer-reviewed
Kawada Shutaro, Hakamata Mayu, Mochizuki Yuji
Journal of Computer Chemistry, Japan16
(
3
)
77
8 2017
-
A New Treatment for Water near the Interface between Lipid Membrane and Silica in Dissipative Particle Dynamics Simulation
Peer-reviewed
Doi Hideo, Okuwaki Koji, Mochizuki Yuji, Ozawa Taku
Journal of Computer Chemistry, Japan16
(
1
)
28
4 2017
-
Fragment molecular orbital (FMO) calculations on DNA by a scaled third-order Møller-Plesset perturbation (MP2.5) scheme
Peer-reviewed
Haruka Yamada, Yuji Mochizuki, Kaori Fukuzawa, Yoshio Okiyama, Yuto Komeiji
Computational and Theoretical Chemistry1101
46
-
54
2 2017
-
Current Status of ABINIT-MP as a FMO Program and Related Works with Machine Learning
Peer-reviewed
Yuji MOCHIZUKI, Kota SAKAKURA, Yoshinobu AKINAGA, Kouichiro KATO, Hiromasa WATANABE, Yoshio OKIYAMA, Tatsuya NAKANO, Yuto KOMEIJI, Akira OKUSAWA, Kaori FUKUZAWA, Shigenori TANAKA
Journal of Computer Chemistry, Japan16
(
5
)
119
-
122
2017
-
A Preliminary Study of Correction for Inter Fragment Interaction Energy (IFIE) between Fragments Sharing Bond Detached Atom (BDA)
Peer-reviewed
Tatsuya Nakano, Yuji Mochidzuki, Kaori Fukuzawa, Yoshio Okiyama, Chiduru Watanabe
Journal of Computer Aided Chemistry18
(
0
)
143
-
148
2017
-
Theoretical Calculations on Cation-capturing ofMacrocyclic Peptoid with Phenyl Rings in Main Chain
Peer-reviewed
KAWADA Shutaro, HAKAMATA Mayu, MOCHIZUKI Yuji
Journal of Computer Chemistry, Japan16
77
-
79
2017
-
フラグメント分子軌道(FMO)計算の結果の自動解析の試み
望月祐志, 奥沢明
計算工学22
3539
-
3542
2017
-
A New Treatment for Water near the Interface between Lipid Membrane and Silica in Dissipative Particle Dynamics Simulation
Peer-reviewed
DOI Hideo, OKUWAKI Koji, MOCHIZUKI Yuji, OZAWA Taku
Journal of Computer Chemistry, Japan16
28
-
31
2017
-
Explicit solvation of a single-stranded DNA, a binding protein, and their complex: a suitable protocol for fragment molecular orbital calculation
Peer-reviewed
Yuto Komeij, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa
Chem-Bio Informatics Journal17
(
0
)
72
-
84
2017
-
Performance Evaluations of Parallelized DFT Calculations with SMASH on Intel Xeon Phi Processor
Peer-reviewed
Sona SAITOU, Yuji MOCHIZUKI, Yutaka YAMAZAKI, Kazuya ISHIMURA
Journal of Computer Chemistry, Japan15
(
4
)
92
-
96
11 2016
-
Evaluations of Molecular Structure and Aromaticity of C5Ch5 and C6Ch6 (Ch=S, Se, Te)
Peer-reviewed
KAWADA Syuutaro, MOCHIZUKI Yuji, NAKANO Katsuhiro
Journal of Computer Chemistry, Japan15
(
4
)
87
-
91
11 2016
-
Practical Usages Of 3D-printer for Scientific Education of Chemistry and Biology
Peer-reviewed
10 2016
-
Fragment Molecular Orbital (FMO) Calculations of Peptoids
Peer-reviewed
KAWADA Shutaro, SAKAGUCHI Masataka, YONEKURA Ibuki, OKUWAKI Kouji, MOCHIZUKI Yuji, FUKUZAWA Kaori
Journal of Computer Chemistry, Japan15
(
3
)
51
-
52
10 2016
-
Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method
Peer-reviewed
Kana Tokuda, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji
Journal of Molecular Graphics and Modelling69
144
-
153
9 2016
-
Performance Evaluations of Parallelized DFT Calculations with SMASH on Intel Xeon Phi Processor
Peer-reviewed
Sona SAITOU, Yuji MOCHIZUKI, Yutaka YAMAZAKI, Kazuya ISHIMURA
Journal of Computer Chemistry, Japan15
(
4
)
92
-
96
2016
-
Evaluations of Molecular Structure and Aromaticity of C<sub>5</sub>Ch<sub>5</sub> and C<sub>6</sub>Ch<sub>6</sub> (Ch=S, Se, Te)
Peer-reviewed
KAWADA Syuutaro, MOCHIZUKI Yuji, NAKANO Katsuhiro
Journal of Computer Chemistry, Japan15
(
4
)
87
-
91
2016
-
化学・生命科学系の理学教育における3Dプリンタの活用事例
Peer-reviewed
望月祐志, 中村昇太, 山中正浩, 山田康之, 工藤光子, 常盤広明, 川上勝, 北本俊二
J. Comp. Chem. Jpn.15
65
-
67
2016
-
Fragment Molecular Orbital (FMO) Calculations of Peptoids
Peer-reviewed
KAWADA Shutaro, SAKAGUCHI Masataka, YONEKURA Ibuki, OKUWAKI Kouji, MOCHIZUKI Yuji, FUKUZAWA Kaori
Journal of Computer Chemistry, Japan15
(
3
)
51
-
52
2016
-
Effects of Water Molecules and Configurations of Neighboring Amino Acid Residues Surrounding DsRed Chromophore on Its Excitation Energy
Peer-reviewed
坂口正貴, 望月祐志, 望月祐志, 渡邉千鶴, 福澤薫, 福澤薫
Journal of Computer Chemistry, Japan (Web)14
(
5
)
12 2015
-
Reversible Structural Changes Accompanying the Two-Electron Redox Reaction of Pt(tacn) (tacn: 1,4,7-triazacyclononane) Complexes
Peer-reviewed
Tohru Wada, Koki Enami, Ryohei Kojima, Tomoki Okada, Yuki Ishikawa, Yuji Miyazato, Ernst Horn, Yuji Mochizuki
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN88
(
9
)
1230
-
1237
9 2015
-
Modeling of hydroxyapatite-peptide interaction based on fragment molecular orbital method
Peer-reviewed
Koichiro Kato, Kaori Fukuzawa, Yuji Mochizuki
CHEMICAL PHYSICS LETTERS629
58
-
64
6 2015
-
ペプチド結合における新規フラグメント分割方法の検証および精度評価
坂口正貴, 福澤薫, 渡邉千鶴, 望月祐志
日本化学会講演予稿集95th
(
2
)
231
11 3 2015
-
Explicit solvation modulates intra- and inter-molecular interactions within DNA: Electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method
Peer-reviewed
Kaori Fukuzawa, Ikuo Kurisaki, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Shigenori Tanaka, Yuto Komeiji
Computational and Theoretical Chemistry1054
29
-
37
2 2015
-
Effects of Water Molecules and Configurations of Neighboring Amino Acid Residues Surrounding DsRed Chromophore on Its Excitation Energy
Peer-reviewed
坂口正貴, 望月祐志, 望月祐志, 渡邉千鶴, 福澤薫, 福澤薫
Journal of Computer Chemistry, Japan (Web)14
(
5
)
155
-
163
2015
-
Implementation of Pair Interaction Energy DecompositionAnalysis and Its Applications to Protein-Ligand Systems
Peer-reviewed
Takayuki TSUKAMOTO, Koichiro KATO, Akifumi KATO, Tatsuya NAKANO, Yuji MOCHIZUKI, Kaori FUKUZAWA
Journal of Computer Chemistry, Japan14
(
1
)
1
-
9
2015
-
Fragment Molecular Orbital-Based Molecular Dynamics Study on Hydrated Ln (III) Ions
Peer-reviewed
Fujiwara Takayuki, Mori Hirotoshi, Komeiji Yuto, Mochizuki Yuji
Proceedings of Computational Science Workshop 2014 (CSW2014)
011001
2015
-
Implementation of Pair Interaction Energy DecompositionAnalysis and Its Applications to Protein-Ligand Systems
Peer-reviewed
Takayuki TSUKAMOTO, Koichiro KATO, Akifumi KATO, Tatsuya NAKANO, Yuji MOCHIZUKI, Kaori FUKUZAWA
Journal of Computer Chemistry, Japan14
(
1
)
1
-
9
2015
-
Optimal damping algorithm for unrestricted Hartree-Fock calculations
Peer-reviewed
Jun-Ichi Yamamoto, Yuji Mochizuki
Chem-Bio Informatics Journal14
14
-
33
13 9 2014
-
Interaction energy analysis on specific binding of influenza virus hemagglutinin to avian and human sialosaccharide receptors: Importance of mutation-induced structural change
Peer-reviewed
Satoshi Anzaki, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka
JOURNAL OF MOLECULAR GRAPHICS & MODELLING53
48
-
58
9 2014
-
Hydration effects on enzyme–substrate complex of nylon oligomer hydrolase: inter-fragment interaction energy study by the fragment molecular orbital method
Peer-reviewed
Hiroyuki Ando, Yasuteru Shigeta, Takeshi Baba, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Masayoshi Nakano
Molecular Physics113
(
3-4
)
319
-
326
8 2014
-
Improved Description of the Orbital Relaxation Effect by Practical Use of the Self-Energy
Peer-reviewed
Masaaki Saitow, Tomonori Ida, Yuji Mochizuki
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY114
(
9
)
577
-
586
5 2014
-
Accuracy of the fragment molecular orbital (FMO) calculations for DNA: Total energy, molecular orbital, and inter-fragment interaction energy
Peer-reviewed
Kaori Fukuzawa, Chiduru Watanabe, Ikuo Kurisaki, Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka, Yuto Komeiji
COMPUTATIONAL AND THEORETICAL CHEMISTRY1034
7
-
16
4 2014
-
フラグメント分子軌道法を用いたspin-component-scaled MP2法に基づくタンパク-リガンド相互作用クラスター解析
甘利真司, 望月祐志, 加藤昭史, 福澤薫, 渡邉千鶴, 沖山佳生, 田中成典, 中野達也
CBI学会誌2
(
4
)
17
-
25
2014
-
Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems
Peer-reviewed
Shigenori Tanaka, Yuji Mochizuki, Yuto Komeiji, Yoshio Okiyama, Kaori Fukuzawa
Phys. Chem. Chem. Phys.16
(
22
)
10310
-
10344
2014
-
Fragment molecular orbital−based molecular dynamics (FMO-MD) simulations on hydrated Cu(II) ion
Peer-reviewed
Yuji Kato, Takayuki Fujiwara, Yuto Komeiji, Tatsuya Nakano, Hirotoshi Mori, Yoshio Okiyama, Yuji Mochizuki
Chem-Bio Informatics Journal14
(
0
)
1
-
13
2014
-
Modeling of peptide–silica interaction based on four-body corrected fragment molecular orbital (FMO4) calculations
Peer-reviewed
Yoshio Okiyama, Takayuki Tsukamoto, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka, Yuji Mochizuki
Chemical Physics Letters566
25
-
31
4 2013
-
Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design
Peer-reviewed
Chiduru Watanabe, Kaori Fukuzawa, Yoshio Okiyama, Takayuki Tsukamoto, Akifumi Kato, Shigenori Tanaka, Yuji Mochizuki, Tatsuya Nakano
Journal of Molecular Graphics and Modelling41
31
-
42
4 2013
-
Importance of spin-orbit coupling effect and solvent effect in electronic transition assignments of Pt-II complexes: In the case of cis/trans-[(PtCl2)-Cl-II(NH3)(2)]
Peer-reviewed
Hirotoshi Mori, Ryohei Kojima, Yuji Mochizuki, Waka Uenohara, Izumi Umezawa, Nobuyuki Matsushita
JOURNAL OF MOLECULAR STRUCTURE1035
218
-
223
3 2013
-
Device, system, method and program for producing fragment model
Peer-reviewed
Mochizuki Yuji, Tsukamoto Takayuki, Fukuzawa Kaori
3 2013
-
Cartesian Gaussianの積分の初期積分の計算
中野達也, 山下勝美, 瀬川勝智, 沖山佳生, 望月祐志
CBI学会誌1
42
-
46
2013
-
フラグメント分子軌道法によるインフルエンザウイルス表面タンパク質の大規模量子化学計算
福澤薫, 望月祐志, 中野達也, 田中成典
CBI学会誌1
25
-
31
2013
-
FMO法における電子相関計算
望月祐志
日本化学会・情報部会31
64
-
72
2013
-
Analysis of Global Ecosystem Ecology by Fragment Molecular Orbital (FMO) Method--Analyses of the interactions between virus hemagglutinins and their receptors--
Peer-reviewed
Maruyama Tadashi, Shimane Yasuhiro, Ohishi Kazue, Iwasawa Misako, Hatada Yuji, Usui Keiko, Takaki Yoshihiro, Yoshida Takao, Tanaka Shigenori, Anzaki Satoshi, other
Annual Report of the Earth Simulator Center April2014
2013
-
Dynamic fragmentation with static fragments (DF/SF) algorithm designed for ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) simulations of polypeptides
Peer-reviewed
Yuto Komeiji, Takayuki Fujiwara, Yoshio Okiyama, Yuji Mochizuki
Chem-Bio Informatics Journal13
(
0
)
45
-
57
2013
-
Ab initio path integral Monte Carlo simulations for water trimer with electron correlation effects
Peer-reviewed
Takatoshi Fujita, Shigenori Tanaka, Takayuki Fujiwara, Masa-Aki Kusa, Yuji Mochizuki, Motoyuki Shiga
COMPUTATIONAL AND THEORETICAL CHEMISTRY997
7
-
13
10 2012
-
Interaction energy calculation system, method and program
Peer-reviewed
Nakano Tatsuya, Mochizuki Yuji, Fukuzawa Kaori
8 2012
-
FMO-MD Simulations on the Hydration of Formaldehyde in Water Solution with Constraint Dynamics
Peer-reviewed
Makoto Sato, Hiroshi Yamataka, Yuto Komeiji, Yuji Mochizuki
CHEMISTRY-A EUROPEAN JOURNAL18
(
31
)
9714
-
9721
7 2012
-
Partial geometry optimization with FMO-MP2 gradient: Application to TrpCage
Peer-reviewed
Takayuki Tsukamoto, Yuji Mochizuki, Naoki Watanabe, Kaori Fukuzawa, Tatsuya Nakano
CHEMICAL PHYSICS LETTERS535
157
-
162
5 2012
-
Differences in hydration between cis- and trans-platin: Quantum insights by ab initio fragment molecular orbital-based molecular dynamics (FMO-MD)
Peer-reviewed
Hirotoshi Mori, Natsumi Hirayama, Yuto Komeiji, Yuji Mochizuki
COMPUTATIONAL AND THEORETICAL CHEMISTRY986
30
-
34
4 2012
-
Excited state calculation for free-base and metalloporphyrins with the partially renormalized polarization propagator approach
Peer-reviewed
Masaaki Saitow, Yuji Mochizuki
CHEMICAL PHYSICS LETTERS525-26
144
-
149
2 2012
-
Efficient Calculation of Fragment Molecular Orbital Method with Continuous Multipole Method
Tatsuya Nakano, Katsumi Yamashita, Katsunori Segawa, Yoshio Okiyama, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka, Yuji Mochidzuki
Journal of Computer Aided Chemistry13
(
0
)
44
-
50
2012
-
New fragmentation of fragment molecular orbital method applicable to fragment based drug design
Peer-reviewed
Watanabe Chiduru, Fukuzawa Kaori, Okiyama Yoshio, Tsukamoto Takayuki, Kato Akifumi, Tanaka Shigenori, Nakano Tatsuya, Mochizuki Yuji
2012
-
Development of the four-body corrected fragment molecular orbital (FMO4) method
Peer-reviewed
Tatsuya Nakano, Yuji Mochizuki, Katsumi Yamashita, Chiduru Watanabe, Kaori Fukuzawa, Katsunori Segawa, Yoshio Okiyama, Takayuki Tsukamoto, Shigenori Tanaka
Chemical Physics Letters523
128
-
133
1 2012
-
Ab Initio Path Integral Molecular Dynamics and Monte Carlo Simulations for Water Trimer and Oligopeptide
Peer-reviewed
Takatoshi Fujita, Masa-Aki Kusa, Takayuki Fujiwara, Yuji Mochizuki, Shigenori Tanaka
ADVANCES IN QUANTUM MONTE CARLO1094
187
-
+
2012
-
Antigen-antibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation
Peer-reviewed
Akio Yoshioka, Kazutomo Takematsu, Ikuo Kurisaki, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Eri Nobusawa, Katsuhisa Nakajima, Shigenori Tanaka
THEORETICAL CHEMISTRY ACCOUNTS130
(
4-6
)
1197
-
1202
12 2011
-
Higher-order correlated calculations based on fragment molecular orbital scheme
Peer-reviewed
Yuji Mochizuki, Katsumi Yamashita, Tatsuya Nakano, Yoshio Okiyama, Kaori Fukuzawa, Naoki Taguchi, Shigenori Tanaka
THEORETICAL CHEMISTRY ACCOUNTS130
(
2-3
)
515
-
530
10 2011
-
Prediction of probable mutations in influenza virus hemagglutinin protein based on large-scale ab initio fragment molecular orbital calculations
Peer-reviewed
Akio Yoshioka, Kaori Fukuzawa, Yuji Mochizuki, Katsumi Yamashita, Tatsuya Nakano, Yoshio Okiyama, Eri Nobusawa, Katsuhisa Nakajima, Shigenori Tanaka
Journal of Molecular Graphics and Modelling30
110
-
119
9 2011
-
4f-in-core model core potentials for trivalent lanthanides
Peer-reviewed
Takayuki Fujiwara, Hirotoshi Mori, Yuji Mochizuki, You Osanai, Eisaku Miyoshi
CHEMICAL PHYSICS LETTERS510
(
4-6
)
261
-
266
7 2011
-
Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme
Peer-reviewed
Yoshio Okiyama, Kaori Fukuzawa, Haruka Yamada, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka
Chemical Physics Letters509
(
1-3
)
67
-
71
6 2011
-
Fragment molecular orbital-based molecular dynamics (FMO-MD) method with MP2 gradient
Peer-reviewed
Yuji Mochizuki, Tatsuya Nakano, Yuto Komeiji, Katsumi Yamashita, Yoshio Okiyama, Hikaru Yoshikawa, Hiroshi Yamataka
Chemical Physics Letters504
(
1-3
)
95
-
99
2 2011
-
Fragment molecular orbital calculations for excitation energies of blue- and yellow-fluorescent proteins
Peer-reviewed
Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano
CHEMICAL PHYSICS LETTERS504
(
1-3
)
76
-
82
2 2011
-
Development of QC2AS- A computer algebra system for symbolic quantum chemical computations
Peer-reviewed
Takeshi Osoekawa, Yuji Mochizuki, Kazuhiro Kyokoyama
Proceedings - 2011 International Conference on Computational Science and Its Applications, ICCSA 2011
102
-
109
2011
-
Fragment molecular orbital (FMO) study on stabilization mechanism of neuro-oncological ventral antigen (NOVA)-RNA complex system
Peer-reviewed
Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM962
(
1-3
)
45
-
55
12 2010
-
Theoretical study of hydration models of trivalent rare-earth ions using model core potentials
Peer-reviewed
Takayuki Fujiwara, Hirotoshi Mori, Yuji Mochizuki, Hiroshi Tatewaki, Eisaku Miyoshi
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM949
(
1-3
)
28
-
35
6 2010
-
Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA)
Peer-reviewed
Yuji Mochizuki, Katsumi Yamashita, Kaori Fukuzawa, Kazutomo Takematsu, Hirofumi Watanabe, Naoki Taguchi, Yoshio Okiyama, Misako Tsuboi, Tatsuya Nakano, Shigenori Tanaka
Chemical Physics Letters493
(
4-6
)
346
-
352
6 2010
-
Flexible ligand recognition of peroxisome proliferator-activated receptor-gamma (PPAR gamma)
Peer-reviewed
Kenji Yamagishi, Keiko Yamamoto, Yuji Mochizuki, Tatsuya Nakano, Sachiko Yamada, Hiroaki Tokiwa
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS20
(
11
)
3344
-
3347
6 2010
-
Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Zn(II) ion
Peer-reviewed
Takayuki Fujiwara, Yuji Mochizuki, Yuto Komeiji, Yoshio Okiyama, Hirotoshi Mori, Tatsuya Nakano, Eisaku Miyoshi
Chemical Physics Letters490
(
1-3
)
41
-
45
4 2010
-
Acceleration of fragment molecular orbital calculations with Cholesky decomposition approach
Peer-reviewed
Yoshio Okiyama, Tatsuya Nakano, Katsumi Yamashita, Yuji Mochizuki, Naoki Taguchi, Shigenori Tanaka
Chemical Physics Letters490
(
1-3
)
84
-
89
4 2010
-
Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Zn(II) ion
Peer-reviewed
Takayuki Fujiwara, Yuji Mochizuki, Yuto Komeiji, Yoshio Okiyama, Hirotoshi Mori, Tatsuya Nakano, Eisaku Miyoshi
Chemical Physics Letters490
(
1-3
)
41
-
45
4 2010
-
Three-body expansion and generalized dynamic fragmentation improve the fragment molecular orbital-based molecular dynamics (FMO-MD)
Peer-reviewed
Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano
CHEMICAL PHYSICS LETTERS484
(
4-6
)
380
-
386
1 2010
-
Theoretical Analysis of the Molecular Mechanism of Stabilization of Nova-RNA Complex System: Fragment Molecular Orbital Method Based Quantum Chemical Calculation For the Effect of the Complex Formation on the Electronic State of Biomacromolecular System
Peer-reviewed
Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka
BIOPHYSICAL JOURNAL98
(
3
)
74A
-
74A
1 2010
-
Gröbner Basis Technique for Algebraic Formulas in Electron Correlation Theories
Peer-reviewed
Osoekawa Takeshi, Shinohara Naoyuki, Mochizuki Yuji, Yokoyama Kazuhiro
Computational Science and Its Applications (ICCSA), 2010 International Conference on
17
2010
-
Does Amination of Formaldehyde Proceed Through a Zwitterionic Intermediate in Water? Fragment Molecular Orbital Molecular Dynamics Simulations by Using Constraint Dynamics
Peer-reviewed
Makoto Sato, Hiroshi Yamataka, Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano
CHEMISTRY-A EUROPEAN JOURNAL16
(
22
)
6430
-
6433
2010
-
1P260 Fragment molecular orbital calculation of the absorption maxima of bacteriorhodopsin and pharaonis phoborhodopsin (Photobiology: Vision & Photoreception, The 48th Annual Meeting of the Biophysical Society of Japan)
Peer-reviewed
Hayashi Tomohiko, Taguchi Naoki, Mochizuki Yuji, Sakurai Minoru
Seibutsu Butsuri50
(
supplement2
)
S65
2010
-
Accuracy of fragmentation in ab initio calculations of hydrated sodium cation
Peer-reviewed
Takatoshi Fujita, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka
CHEMICAL PHYSICS LETTERS478
(
4-6
)
295
-
300
8 2009
-
Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding
Peer-reviewed
Kazutomo Takematsu, Kaori Fukuzawa, Katsumi Omagari, Setsuko Nakajima, Katsuhisa Nakajima, Yuji Mochizuki, Tatsuya Nakano, Hirofumi Watanabe, Shigenori Tanaka
JOURNAL OF PHYSICAL CHEMISTRY B113
(
15
)
4991
-
4994
4 2009
-
Application of Dyson-corrected second-order perturbation theories
Peer-reviewed
Yuji Mochizuki
CHEMICAL PHYSICS LETTERS472
(
1-3
)
143
-
148
4 2009
-
Ab initio quantum-chemical study on emission spectra of bioluminescent luciferases by fragment molecular orbital method
Peer-reviewed
Ayumu Tagami, Nobuhiro Ishibashi, Dai-ichiro Kato, Naoki Taguchi, Yuji Mochizuki, Hirofumi Watanabe, Mika Ito, Shigenori Tanaka
CHEMICAL PHYSICS LETTERS472
(
1-3
)
118
-
123
4 2009
-
Fragment molecular orbital-based molecular dynamics (FMO-MD), a quantum simulation tool for large molecular systems
Peer-reviewed
Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano, Dmitri G. Fedorov
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM898
(
1-3
)
2
-
7
3 2009
-
Fragment Molecular Orbital Calculations on Red Fluorescent Proteins (DsRed and mFruits)
Peer-reviewed
Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Kaori Fukuzawa, Takeshi Ishikawa, Minoru Sakurai, Shigenori Tanaka
JOURNAL OF PHYSICAL CHEMISTRY B113
(
4
)
1153
-
1161
1 2009
-
Fragment Molecular Orbital Method-Based Molecular Dynamics (FMO-MD) as a Simulator for Chemical Reactions in Explicit Solvation
Peer-reviewed
Yuto Komeiji, Takeshi Ishikawa, Yuji Mochizuki, Hiroshi Yamataka, Tatsuya Nakano
JOURNAL OF COMPUTATIONAL CHEMISTRY30
(
1
)
40
-
50
1 2009
-
Developments of FMO methodology and graphical user interface in ABINIT-MP
Peer-reviewed
Nakano Tatsuya, Mochizuki Yuji, Kato Akifumi, Fukuzawa Kaori, Ishikawa Takeshi, Amari Shinji, Kurisaki Ikuo, Tanaka Shigenori
The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems
37
-
62
2009
-
Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations
Peer-reviewed
Yoshio Okiyama, Hirofumi Watanabe, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Takeshi Ishikawa, Kuniyoshi Ebina, Shigenori Tanaka
Chemical Physics Letters467
(
4-6
)
417
-
423
1 2009
-
Analysis of Mutation Mechanisms of Influenza Virus Based on the Fragment Molecular Orbital Method
Peer-reviewed
Tanaka Shigenori, Mochizuki Yuji, Fukuzawa Kaori, Yamashita Katsumi, Nakano Tatsuya
Annual Report of the Earth Simulator Center April2010
2009
-
7 Application of the FMO Method to Specific Molecular Recognition of Biomacromolecules
Peer-reviewed
Fukuzawa Kaori, Mochizuki Yuji, Nakano Tatsuya, Tanaka Shigenori
The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems
133
-
169
2009
-
4 Excited States of Photoactive Proteins by Configuration Interaction Studies
Peer-reviewed
Mochizuki Yuji, Nakano Tatsuya, Taguchi Naoki, Tanaka Shigenori
The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems
63
-
89
2009
-
3P-063 Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding (Protein: Function, 2SP6 Towards Supercomputiong for Electronic Structures of Biological
Peer-reviewed
Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori
Seibutsu Butsuri49
(
supplement
)
S161
2009
-
2SP6-07 Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding (2SP6 Towards Supercomputing for Electronic Structures of Biological Macromolecules, The
Peer-reviewed
Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori
Seibutsu Butsuri49
(
supplement
)
S15
2009
-
3P-063 Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding(Protein:Function,2SP6 Towards Supercomputiong for Electronic Structures of Biological Macromolecules,Symposia,The 47th Annual Meeting of the Biophysical Society of Japan)
Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori
Seibutsu Butsuri49
S161
2009
-
An application of fragment interaction analysis based on local MP2
Peer-reviewed
Takeshi Ishikawa, Yuji Mochizuki, Shinji Amari, Tatsuya Nakano, Shigenori Tanaka, Kiyoshi Tanaka
CHEMICAL PHYSICS LETTERS463
(
1-3
)
189
-
194
9 2008
-
Ab initio fragment molecular orbital study of molecular interactions in liganded retinoid X receptor: Specification of residues associated with ligand inducible information transmission
Peer-reviewed
Mika Ito, Kaori Fukuzawa, Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka
JOURNAL OF PHYSICAL CHEMISTRY B112
(
38
)
12081
-
12094
9 2008
-
COMP 246-Simulation study of RNA-binding protein by fragment molecular orbital (FMO) method
Peer-reviewed
Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY236
8 2008
-
Theoretical analysis of binding specificity of influenza viral hemagglutinin to avian and human receptors based on the fragment molecular orbital method
Peer-reviewed
Tatsunori Iwata, Kaori Fukuzawa, Katsuhisa Nakajima, Sachiko Aida-Hyugaji, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka
COMPUTATIONAL BIOLOGY AND CHEMISTRY32
(
3
)
198
-
211
6 2008
-
Large scale FMO-MP2 calculations on a massively parallel-vector computer
Peer-reviewed
Yuji Mochizuki, Katsumi Yamashita, Tadashi Murase, Tatsuya Nakano, Kaori Fukuzawa, Kazutomo Takematsu, Hirofumi Watanabe, Shigenori Tanaka
CHEMICAL PHYSICS LETTERS457
(
4-6
)
396
-
403
5 2008
-
Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid X receptor and its coactivator; Part II: Influence of mutations in transcriptional activation function 2 activating domain core on the molecular interactions
Peer-reviewed
Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka
JOURNAL OF PHYSICAL CHEMISTRY A112
(
10
)
1986
-
1998
3 2008
-
Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid X receptor and its coactivator; Part II: Influence of mutations in transcriptional activation function 2 activating domain core on the molecular interactions
Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka
JOURNAL OF PHYSICAL CHEMISTRY A112
(
10
)
1986
-
1998
3 2008
-
How does an S(N)2 reaction take place in solution? Full ab initio MD simulations for the hydrolysis of the methyl diazonium ion
Peer-reviewed
Makoto Sato, Hiroshi Yamataka, Yuto Komeiji, Yuji Mochizuki, Takeshi Ishikawa, Tatsuya Nakano
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY130
(
8
)
2396
-
2397
2 2008
-
A practical use of self-energy shift for the description of orbital relaxation
Peer-reviewed
Yuji Mochizuki
CHEMICAL PHYSICS LETTERS453
(
1-3
)
109
-
116
2 2008
-
フラグメント分子軌道法によるホタルルシフェラーゼの発光特性に関する理論的研究
田上歩, 石橋延裕, 加藤太一郎, 田口尚貴, 望月祐志, 渡邉博文, 伊藤三香, 田中成典
J. Comp. Aided Chem9
47
-
54
2008
-
Research on Innovative Simulation Software
Peer-reviewed
Kato Chisachi, Tsubokura Makoto, Yamade Yoshinobu, Mochizuki Yuji, Yamashita Katsumi, Nakano Tatsuya, Yamamoto Takenori, Yamasaki Takahiro, Ohno Takahisa
Annual Report of the Earth Simulator Center April2008
2008
-
Infantosi, AFC, 5, 273 Ioannidis, JPA, 39 Iwata, T., 198 Ji, Z., 243
Peer-reviewed
Josic K, Kandemir-Cavas C, Kanwar JR, Karabencheva TG, Khaladkar M, Khoshmanesh K, Kim H, Kim JR, Kiran K, Komeiji Y
Computational Biology and Chemistry32
470
2008
-
Multi-reference calculations of nitric oxide dimer
Peer-reviewed
Naoki Taguchi, Yuji Mochizuki, Takeshi Ishikawa, Kiyoshi Tanaka
CHEMICAL PHYSICS LETTERS451
(
1-3
)
31
-
36
1 2008
-
Fragment interaction analysis based on local MP2
Peer-reviewed
Takeshi Ishikawa, Yuji Mochizuki, Shinji Amari, Tatsuya Nakano, Hiroaki Tokiwa, Shigenori Tanaka, Kiyoshi Tanaka
THEORETICAL CHEMISTRY ACCOUNTS118
(
5-6
)
937
-
945
12 2007
-
Fragment interaction analysis based on local MP2
Takeshi Ishikawa, Yuji Mochizuki, Shinji Amari, Tatsuya Nakano, Hiroaki Tokiwa, Shigenori Tanaka, Kiyoshi Tanaka
THEORETICAL CHEMISTRY ACCOUNTS118
(
5-6
)
937
-
945
12 2007
-
Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method
Peer-reviewed
Ikuo Kurisaki, Kaori Fukuzawa, Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano, Janine Imada, Arleta Chmielewski, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka
BIOPHYSICAL CHEMISTRY130
(
1-2
)
1
-
9
10 2007
-
Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method
Ikuo Kurisaki, Kaori Fukuzawa, Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano, Janine Imada, Arleta Chmielewski, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka
BIOPHYSICAL CHEMISTRY130
(
1-2
)
1
-
9
10 2007
-
Modification for spin-adapted version of configuration interaction singles with perturbative doubles
Peer-reviewed
Yuji Mochizuki, Kiyoshi Tanaka
Chemical Physics Letters443
(
4-6
)
389
-
397
6 8 2007
-
Modification for spin-adapted version of configuration interaction singles with perturbative doubles
Yuji Mochizuki, Kiyoshi Tanaka
CHEMICAL PHYSICS LETTERS443
(
4-6
)
389
-
397
8 2007
-
Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme
Peer-reviewed
Yuji Mochizuki, Kiyoshi Tanaka, Katsumi Yamashita, Takeshi Ishikawa, Tatsuya Nakano, Shinji Amari, Katsunori Segawa, Tadashi Murase, Hiroaki Tokiwa, Minoru Sakurai
THEORETICAL CHEMISTRY ACCOUNTS117
(
4
)
541
-
553
4 2007
-
Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid x receptor and its coactivator: Roles of helix 12 in the coactivator binding mechanism
Peer-reviewed
Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka
JOURNAL OF PHYSICAL CHEMISTRY B111
(
13
)
3525
-
3533
4 2007
-
Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid x receptor and its coactivator: Roles of helix 12 in the coactivator binding mechanism
Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka
JOURNAL OF PHYSICAL CHEMISTRY B111
(
13
)
3525
-
3533
4 2007
-
Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme
Yuji Mochizuki, Kiyoshi Tanaka, Katsumi Yamashita, Takeshi Ishikawa, Tatsuya Nakano, Shinji Amari, Katsunori Segawa, Tadashi Murase, Hiroaki Tokiwa, Minoru Sakurai
THEORETICAL CHEMISTRY ACCOUNTS117
(
4
)
541
-
553
4 2007
-
A fully quantum mechanical simulation study on the lowest n-π* state of hydrated formaldehyde
Yuji Mochizuki, Yuto Komeiji, Takeshi Ishikawa, Tatsuya Nakano, Hiroshi Yamataka
Chemical Physics Letters437
(
1-3
)
66
-
72
22 3 2007
-
A graphical symmetric group approach for a spin adapted full configuration interaction: partitioning of a configuration graph into sets of closed-shell and open-shell graphs
Peer-reviewed
Kiyoshi Tanaka, Yuji Mochizuki, Takeshi Ishikawa, Hidemi Terashima, Hiroaki Tokiwa
THEORETICAL CHEMISTRY ACCOUNTS117
(
3
)
397
-
405
3 2007
-
A fully quantum mechanical simulation study on the lowest n-pi(*) state of hydrated formaldehyde
Peer-reviewed
Yuji Mochizuki, Yuto Komeiji, Takeshi Ishikawa, Tatsuya Nakano, Hiroshi Yamataka
CHEMICAL PHYSICS LETTERS437
(
1-3
)
66
-
72
3 2007
-
Frontier Simulation Software for Industrial Science
Makoto Tsubokura, Yuji Mochizuki, Katsumi Yamashita, Tadashi Murase, Kenji Yamagishi, Hiroaki Tokiwa, Tatsuya Nakano, Takenori Yamamoto, Takahisa Ohno
Annual Report of the Earth Simulator Center April 2005 - March 200656
(
4
)
299
-
304
2007
-
On Mechanism of Enhanced Fluorescence in Green Fluorescent Protein
Peer-reviewed
STARIKOV EVGENI B, Panas Itai, MOCHIZUKI YUJI, TANAKA SHIGENORI, Luo Yi, AA}gren Hans
Biophysical Reviews and Letters2
(
03n04
)
221
-
227
2007
-
Fragment molecular orbital calculations on red fluorescent protein (DsRed)
Peer-reviewed
Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Takeshi Ishikawa, Kiyoshi Tanaka, Minoru Sakurai, Shigenori Tanaka
CHEMICAL PHYSICS LETTERS433
(
4-6
)
360
-
367
1 2007
-
Application of the fragment molecular orbital method for determination of atomic charges on polypeptides
Peer-reviewed
Yoshio Okiyama, Hirofumi Watanabe, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Takeshi Ishikawa, Shigenori Tanaka, Kuniyoshi Ebina
Chemical Physics Letters449
(
4-6
)
329
-
335
2007
-
Ab initio FMO-MD method reimplemented and applied to pure water
Peer-reviewed
Yuto Komeiji, Takeshi Ishikawa, Yuji Mochizuki, Hiroshi Yamataka, Tatsuya Nakano
COMPUTATION IN MODERN SCIENCE AND ENGINEERING VOL 2, PTS A AND B2
(
2
)
1261
-
+
2007
-
2P058 Theoretical study on the sequence specific recognition mechanism of Pumilio RNA-binding domain by Fragment Molecular Orbital (FMO) method (Proteins-structure and structure-function relationship, Poster Presentations)
Peer-reviewed
Kurisaki Ikuo, Fukuzawa Kaori, Nakano Tatsuya, Mochizuki Yuji, Watanabe Hirofumi, Tanaka Shigenori
Seibutsu Butsuri47
(
supplement
)
S127
2007
-
Fragment molecular orbital calculations on red fluorescent protein (DsRed)
Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Takeshi Ishikawa, Kiyoshi Tanaka, Minoru Sakurai, Shigenori Tanaka
CHEMICAL PHYSICS LETTERS433
(
4-6
)
360
-
367
1 2007
-
Application of Fragment Molecular Orbital (FMO) Method to Nano-Bio Field
NAKANO Tatsuya, MOCHIZUKI Yuji, AMARI Shinji, KOBAYASHI Masato, FUKUZAWA Kaori, TANAKA Shigenori
Journal of Computer Chemistry, Japan6
(
3
)
173
-
184
1 1 2007
-
Applications of the Fragment Molecular Orbital Method for Bio-Macromolecules
FUKUZAWA Kaori, NAKANO Tatsuya, KATO Akifumi, MOCHIZUKI Yuji, TANAKA Shigenori
Journal of Chemical Software6
(
3
)
185
-
198
1 1 2007
-
A graphical symmetric group approach for a spin adapted full configuration interaction
望月 祐志
K. Tanaka, Y. Mochizuki, T. Ishikawa, H. Terashima, and H. Tokiwa,
(
117
)
397
-
405
1 1 2007
-
Erratum: Intra- and intermodular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study (Journal of Computational Chemistry (2006) 27 (948))
Peer-reviewed
Fukuzawa, K., Komeiji, Y., Mochizuki, Y., Kato, A., Nakano, T., Tanaka, S.
Journal of Computational Chemistry28
(
13
)
2007
-
Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method (vol 110, pg 24276, 2006)
Peer-reviewed
Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka, Kazuo Kitaura, Tatsuya Nakano
JOURNAL OF PHYSICAL CHEMISTRY B110
(
47
)
24276
-
24276
11 2006
-
Application of fragment molecular orbital scheme to silicon-containing systems
Peer-reviewed
Takeshi Ishikawa, Yuji Mochizuki, Kenji Imamura, Tatsuya Nakano, Hirotoshi Mori, Hiroaki Tokiwa, Kiyoshi Tanaka, Eisaku Miyoshi, Shigenori Tanaka
CHEMICAL PHYSICS LETTERS430
(
4-6
)
361
-
366
10 2006
-
Application of fragment molecular orbital scheme to silicon-containing systems
Takeshi Ishikawa, Yuji Mochizuki, Kenji Imamura, Tatsuya Nakano, Hirotoshi Mori, Hiroaki Tokiwa, Kiyoshi Tanaka, Eisaku Miyoshi, Shigenori Tanaka
CHEMICAL PHYSICS LETTERS430
(
4-6
)
361
-
366
10 2006
-
Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method
Peer-reviewed
Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka, Kazuo Kitaura, Tatsuya Nakano
JOURNAL OF PHYSICAL CHEMISTRY B110
(
32
)
16102
-
16110
8 2006
-
Fragment molecular orbital calculations on large scale systems containing heavy metal atom
Peer-reviewed
Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Hirotoshi Mori, Hiroaki Honda, Takatoshi Fujita, Hiroaki Tokiwa, Shigenori Tanaka, Yuto Komeiji, Kaori Fukuzawa, Kiyoshi Tanaka, Eisaku Miyoshi
CHEMICAL PHYSICS LETTERS427
(
1-3
)
159
-
165
8 2006
-
Fragment molecular orbital calculations on large scale systems containing heavy metal atom
Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Hirotoshi Mori, Hiroaki Honda, Takatoshi Fujita, Hiroaki Tokiwa, Shigenori Tanaka, Yuto Komeiji, Kaori Fukuzawa, Kiyoshi Tanaka, Eisaku Miyoshi
CHEMICAL PHYSICS LETTERS427
(
1-3
)
159
-
165
8 2006
-
Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method
Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka, Kazuo Kitaura, Tatsuya Nakano
JOURNAL OF PHYSICAL CHEMISTRY B110
(
32
)
16102
-
16110
8 2006
-
Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study
Peer-reviewed
K Fukuzawa, Y Komeiji, Y Mochizuki, A Kato, T Nakano, S Tanaka
JOURNAL OF COMPUTATIONAL CHEMISTRY27
(
8
)
948
-
960
6 2006
-
Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study
K Fukuzawa, Y Komeiji, Y Mochizuki, A Kato, T Nakano, S Tanaka
JOURNAL OF COMPUTATIONAL CHEMISTRY27
(
8
)
948
-
960
6 2006
-
Dynamic polarizability calculation with fragment molecular orbital scheme
Peer-reviewed
Y Mochizuki, T Ishikawa, K Tanaka, H Tokiwa, T Nakano, S Tanaka
CHEMICAL PHYSICS LETTERS418
(
4-6
)
418
-
422
2 2006
-
Dynamic polarizability calculation with fragment molecular orbital scheme
Y Mochizuki, T Ishikawa, K Tanaka, H Tokiwa, T Nakano, S Tanaka
CHEMICAL PHYSICS LETTERS418
(
4-6
)
418
-
422
2 2006
-
VISCANA: Visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening
Peer-reviewed
S Amari, M Aizawa, JW Zhang, K Fukuzawa, Y Mochizuki, Y Iwasawa, K Nakata, H Chuman, T Nakano
JOURNAL OF CHEMICAL INFORMATION AND MODELING46
(
1
)
221
-
230
1 2006
-
Revolutionary Simulation Software for 21st Century
Peer-reviewed
Kato Chisachi, Tsubokura Makoto, Yamade Yoshinobu, Arakawa Takamichi, Mochizuki Yuji, Yamashita Katsumi, Murase Tadashi, Nakano Tatsuya, Yamamoto Takenori, Ohno Takahisa, o, h
Annual Report of the Earth Simulator Center April2007
2006
-
Developments and applications of ABINIT-MP software based on the fragment molecular orbital method
Peer-reviewed
Tatsuya Nakano, Yuji Mochizuki, Kaori Fukuzawa, Shinji Amari, Shigenori Tanaka
Modern Methods for Theoretical Physical Chemistry of Biopolymers
39
-
52
2006
-
VISCANA: Visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening
S Amari, M Aizawa, JW Zhang, K Fukuzawa, Y Mochizuki, Y Iwasawa, K Nakata, H Chuman, T Nakano
JOURNAL OF CHEMICAL INFORMATION AND MODELING46
(
1
)
221
-
230
1 2006
-
A size-extensive modification of super-CI for orbital relaxation
Peer-reviewed
Yuji Mochizuki
Chemical Physics Letters410
(
1-3
)
165
-
171
10 7 2005
-
1A configuration analysis for fragment interaction
Peer-reviewed
Y Mochizuki, K Fukuzawa, A Kato, S Tanaka, K Kitaura, T Nakano
CHEMICAL PHYSICS LETTERS410
(
4-6
)
247
-
253
7 2005
-
A size-extensive modification of super-Cl for orbital relaxation
Y Mochizuki
CHEMICAL PHYSICS LETTERS410
(
1-3
)
165
-
171
7 2005
-
1A configuration analysis for fragment interaction
Y Mochizuki, K Fukuzawa, A Kato, S Tanaka, K Kitaura, T Nakano
CHEMICAL PHYSICS LETTERS410
(
4-6
)
247
-
253
7 2005
-
Configuration interaction singles method with multilayer fragment molecular orbital scheme
Peer-reviewed
Y Mochizuki, S Koikegami, S Amari, K Segawa, K Kitaura, T Nakano
CHEMICAL PHYSICS LETTERS406
(
4-6
)
283
-
288
5 2005
-
Configuration interaction singles method with multilayer fragment molecular orbital scheme
Y Mochizuki, S Koikegami, S Amari, K Segawa, K Kitaura, T Nakano
CHEMICAL PHYSICS LETTERS406
(
4-6
)
283
-
288
5 2005
-
Frontier Simulation Software for Industrial Science
Peer-reviewed
Kato Chisachi, Tsubokura Makoto, Mochizuki Yuji, Yamashita Katsumi, Murase Tadashi, Yamagishi Kenji, Tokiwa Hiroaki, Nakano Tatsuya, Yamamoto Takenori, Ohno Takahisa
Annual Report of the Earth Simulator Center April2006
(
4
)
2005
-
Fragment Molecular Orbital Study on Molecular Interaction between Estrogen Receptor and Their Ligands
FUKUZAWA, MOCHIZUKI, TANAKA, AMARI, KITAURA, AND, Nakano
Proceedings of 7th Congress of the World Association of Theoretically Oriented Chemists (WATOC) (Cape Town, South Africa)ES-P23,
2005
-
A parallelized integral-direct second-order Moller-Plesset perturbation theory method with a fragment molecular orbital scheme
Peer-reviewed
Y Mochizuki, T Nakano, S Koikegami, S Tanimori, Y Abe, U Nagashima, K Kitaura
THEORETICAL CHEMISTRY ACCOUNTS112
(
5-6
)
442
-
452
12 2004
-
A parallelized integral-direct second-order Moller-Plesset perturbation theory method with a fragment molecular orbital scheme
Y Mochizuki, T Nakano, S Koikegami, S Tanimori, Y Abe, U Nagashima, K Kitaura
THEORETICAL CHEMISTRY ACCOUNTS112
(
5-6
)
442
-
452
12 2004
-
Large scale MP2 calculations with fragment molecular orbital scheme
Peer-reviewed
Y Mochizuki, S Koikegami, T Nakano, S Amari, K Kitaura
CHEMICAL PHYSICS LETTERS396
(
4-6
)
473
-
479
10 2004
-
Large scale MP2 calculations with fragment molecular orbital scheme
Y Mochizuki, S Koikegami, T Nakano, S Amari, K Kitaura
CHEMICAL PHYSICS LETTERS396
(
4-6
)
473
-
479
10 2004
-
Development of integral transformation modules for correlated calculations
Y. Mochizuki, U. Nagashima
J. Comp. Chem. Jpn.3
(
1
)
1
-
12
2004
-
Comparative study of dehydrogenation at Pt(111)/water and Pt(111)/vacuum of methanol interfaces
Peer-reviewed
Y Okamoto, O Sugino, Y Mochizuki, T Ikeshoji, Y Morikawa
CHEMICAL PHYSICS LETTERS377
(
1-2
)
236
-
242
8 2003
-
Comparative study of dehydrogenation at Pt(111)/water and Pt(111)/vacuum of methanol interfaces
Y Okamoto, O Sugino, Y Mochizuki, T Ikeshoji, Y Morikawa
CHEMICAL PHYSICS LETTERS377
(
1-2
)
236
-
242
8 2003
-
Prolapses in four-component relativistic Gaussian basis sets
Peer-reviewed
H Tatewaki, T Koga, Y Mochizuki
CHEMICAL PHYSICS LETTERS375
(
3-4
)
399
-
405
7 2003
-
Prolapses in four-component relativistic Gaussian basis sets
H Tatewaki, T Koga, Y Mochizuki
CHEMICAL PHYSICS LETTERS375
(
3-4
)
399
-
405
7 2003
-
Ab initio study on the structures of Th(IV) hydrate and its hydrolysis products in aqueous solution
Peer-reviewed
S Tsushima, TX Yang, Y Mochizuki, Y Okamoto
CHEMICAL PHYSICS LETTERS375
(
1-2
)
204
-
212
6 2003
-
Ab initio study on the structures of Th(IV) hydrate and its hydrolysis products in aqueous solution
S Tsushima, TX Yang, Y Mochizuki, Y Okamoto
CHEMICAL PHYSICS LETTERS375
(
1-2
)
204
-
212
6 2003
-
Theoretical study of hydrolysis reactions of tetravalent thorium ion
Peer-reviewed
Y Okamoto, Y Mochizuki, S Tsushima
CHEMICAL PHYSICS LETTERS373
(
1-2
)
213
-
217
5 2003
-
On the electronic structure of CmFn (n=1-4) by all-electron Dirac-Hartree-Fock calculations
Peer-reviewed
Y Mochizuki, H Tatewaki
JOURNAL OF CHEMICAL PHYSICS118
(
20
)
9201
-
9207
5 2003
-
Theoretical study of hydrolysis reactions of tetravalent thorium ion
Y Okamoto, Y Mochizuki, S Tsushima
CHEMICAL PHYSICS LETTERS373
(
1-2
)
213
-
217
5 2003
-
On the electronic structures of Th4+ and Ac3+ hydrate models
Peer-reviewed
Yuji Mochizuki, Satoru Tsushima
Chemical Physics Letters372
(
1-2
)
114
-
120
22 4 2003
-
On the electronic structures of Th4+ and Ac3+ hydrate models
Y Mochizuki, S Tsushima
CHEMICAL PHYSICS LETTERS372
(
1-2
)
114
-
120
4 2003
-
Comments on relativistic basis sets
Peer-reviewed
H Tatewaki, Y Mochizuki
THEORETICAL CHEMISTRY ACCOUNTS109
(
1
)
40
-
42
2 2003
-
Comments on relativistic basis sets
Hiroshi Tatewaki, Yuji Mochizuki
Theoretical Chemistry Accounts109
(
1
)
40
-
42
1 2 2003
-
Electric structure calculations on heavy element systems using the DIRAC code
Peer-reviewed
Mochizuki Yuji
2003
-
On the electronic of CmFn(n=1-4) by all-electron Dirac -Hartree-Fock calculations
望月 祐志
(不明)
(
118
)
9201
-
9207
1 1 2003
-
Four-component relativistic calculations on the mono-ammine complexes of trivalent f0, f7, and f14 ions
Yuji Mochizuki, Yasuharu Okamoto
Chemical Physics Letters359
(
3-4
)
331
-
336
20 6 2002
-
Four-component relativistic calculations on the mono-ammine complexes of trivalent f(0), f(7), and f(14) ions
Peer-reviewed
Y Mochizuki, Y Okamoto
CHEMICAL PHYSICS LETTERS359
(
3-4
)
331
-
336
6 2002
-
On the electronic structure of Cm(H2O)(n)(3+) (n=1,2,4,6) by all-electron Dirac-Hartree-Fock calculations
Peer-reviewed
Y Mochizuki, H Tatewaki
JOURNAL OF CHEMICAL PHYSICS116
(
20
)
8838
-
8842
5 2002
-
On the electronic structure of Cm(H2O)(n)(3+) (n=1,2,4,6) by all-electron Dirac-Hartree-Fock calculations
Y Mochizuki, H Tatewaki
JOURNAL OF CHEMICAL PHYSICS116
(
20
)
8838
-
8842
5 2002
-
Vectorization of direct Fock matrix construction in DIRAC-DHF calculations
Peer-reviewed
Y Mochizuki, M Matsumura, T Yokura, Y Hirahara, T Imamura
JOURNAL OF NUCLEAR SCIENCE AND TECHNOLOGY39
(
2
)
195
-
199
2 2002
-
Size, order, and dimensional relations for silicon cluster polarizabilities
Peer-reviewed
B Jansik, B Schimmelpfennig, P Norman, Y Mochizuki, Y Luo, H Agren
JOURNAL OF PHYSICAL CHEMISTRY A106
(
2
)
395
-
399
1 2002
-
Ab initio MO studies on the hydration of trivalent curium ion
Peer-reviewed
Yuji Mochizuki, Hiroshi Tatewaki, Yasuharu Okamoto
Journal of Nuclear Science and Technology39
(
sup3
)
418
-
421
2002
-
Size, order, and dimensional relations for silicon cluster polarizabilities
B Jansik, B Schimmelpfennig, P Norman, Y Mochizuki, Y Luo, H Agren
JOURNAL OF PHYSICAL CHEMISTRY A106
(
2
)
395
-
399
1 2002
-
Vectorization of direct fock matrix construction in DIRAC-DHF calculations
Yuji Mochizuki, Masayuki Matsumura, Tetsui-Chi Yokura, Yukio Hirahara, Toshiyuki Imamura
Journal of Nuclear Science and Technology39
(
2
)
195
-
199
2002
-
Ab initio MO studies on the hydration of trivalent curium ion
Yuji Mochizuki, Hiroshi Tatewaki, Yasuharu Okamoto
Journal of Nuclear Science and Technology39
(
3
)
418
-
421
2002
-
Modification of nonrelativistic gaussian basis sets for relativistic calculations
Hiroshi Tatewaki, Yuji Mochizuki, Toshikatsu Koga, Jacek Karwowski
Journal of Chemical Physics115
(
20
)
9160
-
9164
22 11 2001
-
Four-component relativistic calculations on the complexes between a water molecule and trivalent lanthanoid and actinoid ions
Yuji Mochizuki, Hiroshi Tatewaki
Chemical Physics273
(
2-3
)
135
-
148
15 11 2001
-
Four-component relativistic calculations on the complexes between a water molecule and trivalent lanthanoid and actinoid ions
Peer-reviewed
Y Mochizuki, H Tatewaki
CHEMICAL PHYSICS273
(
2-3
)
135
-
148
11 2001
-
Modification of nonrelativistic Gaussian basis sets for relativistic calculations
Peer-reviewed
H Tatewaki, Y Mochizuki, T Koga, J Karwowski
JOURNAL OF CHEMICAL PHYSICS115
(
20
)
9160
-
9164
11 2001
-
Vapor-liquid equilibrium data for the four binary systems containing fluorocarbon, hydrofluorocarbon, and fluorinated ethers at 101.3 kPa
Peer-reviewed
K. Tochigi, T. Satou, K. Kurihara, K. Ochi, H. Yamamoto, Y. Mochizuki, T. Sako
Journal of Chemical and Engineering Data46
(
4
)
913
-
917
7 2001
-
HF-STEX and RASSCF calculations on nitrogen K-shell X-ray absorption of purine base and its derivative
Peer-reviewed
Y Mochizuki, H Koide, T Imamura, H Takemiya
JOURNAL OF SYNCHROTRON RADIATION8
(
2
)
1003
-
1005
3 2001
-
Polarizability of silicon clusters
Peer-reviewed
Y Mochizuki, H Agren
CHEMICAL PHYSICS LETTERS336
(
5-6
)
451
-
456
3 2001
-
HF-STEX and RASSCF calculations nitrogen K-shell X-ray absorption of purine base and its derivative
望月 祐志
(不明)
(
8
)
1003
-
1005
1 1 2001
-
Polarizability of silicon clusters
望月 祐志
(不明)
(
273
)
135
-
148
1 1 2001
-
A theoretical investigation of sulphur K-shell X-ray absorption of cysteine
Peer-reviewed
Y Mochizuki, H Agren, LGM Pettersson, Carravetta, V
CHEMICAL PHYSICS LETTERS309
(
3-4
)
241
-
248
8 1999
-
Multireference coupled-pair approximation study of the CuSi molecule
Peer-reviewed
M Tomonari, Y Mochizuki, K Tanaka
THEORETICAL CHEMISTRY ACCOUNTS101
(
5
)
332
-
335
4 1999
-
Theoretical investigation of the GaF molecule and its positive ion
Peer-reviewed
Y Mochizuki, K Tanaka
THEORETICAL CHEMISTRY ACCOUNTS101
(
4
)
257
-
261
3 1999
-
Theoretical spectroscopic constants of the GaN molecule
Peer-reviewed
Y Mochizuki, K Tanaka
THEORETICAL CHEMISTRY ACCOUNTS101
(
4
)
292
-
296
3 1999
-
MULTI-REFERENCE COUPLED PAIR APPROXIMATION: a state-universal approach of a CEPA type variant of MRSDCI
Peer-reviewed
Tanaka Kiyoshi, Sakai Takeo, Mochizuki Yuji
Recent Advances in Multireference Methods4
95
1999
-
Molecular Orbital Study on the Oxidative Decomposition of Hfc-32
Peer-reviewed
Mochizuki Yuji
Data/Code/Japan atomic energy research institute (Tokyo)99
015
1999
-
Theoretical study of the spectroscopic constants of low-lying states of Ga-2
Peer-reviewed
TK Ghosh, K Tanaka, Y Mochizuki
THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE451
(
1-2
)
61
-
71
9 1998
-
Precise control of pn-junction profiles for GaN-based LD structures using GaN substrates with low dislocation densities
Peer-reviewed
N Kuroda, C Sasaoka, A Kimura, A Usui, Y Mochizuki
JOURNAL OF CRYSTAL GROWTH189
551
-
555
6 1998
-
Theoretical investigation on the GaH molecule and its positive ion
Peer-reviewed
Y Mochizuki, K Tanaka
THEORETICAL CHEMISTRY ACCOUNTS99
(
2
)
88
-
94
4 1998
-
Determination of valence band splitting parameters in GaN
Peer-reviewed
AA Yamaguchi, Y Mochizuki, H Sunakawa, A Usui
JOURNAL OF APPLIED PHYSICS83
(
8
)
4542
-
4544
4 1998
-
Uniaxial stress effects on valence band structures of GaN
Peer-reviewed
AA Yamaguchi, Y Mochizuki, C Sasaoka, A Kimura, M Nido, A Usui
NITRIDE SEMICONDUCTORS482
893
-
898
1998
-
A CSF-based multi-reference coupled pair approximation III. An application to F2, As2 and As+ 2
Peer-reviewed
Tanaka Kiyoshi, Mochizuki Yuji
Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)98
(
4
)
165
1998
-
Program linkage method for using dummy arguments to link program having hierarchical structure
Peer-reviewed
Takada Toshikazu, Mochizuki Yuji
10 1997
-
Computational study of the spectroscopic constants of the ground state of the As-2 molecule
Peer-reviewed
Y Mochizuki, K Tanaka
CHEMICAL PHYSICS LETTERS274
(
1-3
)
264
-
268
8 1997
-
Reflectance spectroscopy on GaN films under uniaxial stress
Peer-reviewed
AA Yamaguchi, Y Mochizuki, C Sasaoka, A Kimura, M Nido, A Usui
APPLIED PHYSICS LETTERS71
(
3
)
374
-
376
7 1997
-
Theoretical study of the surface reaction mechanism of GaN with HCl
Peer-reviewed
Y Okamoto, T Takada, Y Mochizuki
JAPANESE JOURNAL OF APPLIED PHYSICS PART 2-LETTERS & EXPRESS LETTERS35
(
12B
)
L1641
-
L1643
12 1996
-
Generalized doubly symbolic formulation for integral-driven direct configuration interaction method
Peer-reviewed
Y Mochizuki, N Nishi, Y Hirahara, T Takada
THEORETICA CHIMICA ACTA93
(
4
)
211
-
233
4 1996
-
Epitaxial growth method of semiconductor crystal and molecular beam epitaxy apparatus for the same
Peer-reviewed
Mochizuki Yuji, Usui Akira, Takada Toshikazu
4 1996
-
Generalized doubly symbolic formulation for integral-driven direct configuration interaction method
Yuji Mochizuki, Naoki Nishi, Yukio Hirahara, Toshikazu Takada
Theoretical Chemistry Accounts93
(
4
)
211
-
233
1996
-
Method for epitaxial growth of semiconductor crystal by using halogenide
Peer-reviewed
Mochizuki Yuji, Chiba Yoshie, Takada Toshikazu, Usui Akira
11 1995
-
ON THE REACTION SCHEME FOR TI/TIN CHEMICAL-VAPOR-DEPOSITION (CVD) PROCESS USING TICL4
Peer-reviewed
Y MOCHIZUKI, Y OKAMOTO, A ISHITANI, K HIROSE, T TAKADA
JAPANESE JOURNAL OF APPLIED PHYSICS PART 2-LETTERS34
(
3A
)
L326
-
L329
3 1995
-
THEORETICAL-STUDY ON THE DIRECT REACTION BETWEEN ASH3 AND SURFACE-ADSORBED GACL
Peer-reviewed
Y MOCHIZUKI, A USUI, S HANDA, T TAKADA
JOURNAL OF CRYSTAL GROWTH148
(
1-2
)
96
-
105
2 1995
-
THEORETICAL-STUDIES ON THE CHLORIDE ALE PROCESS
Peer-reviewed
Y MOCHIZUKI, T TAKADA, A USUI
APPLIED SURFACE SCIENCE82-3
200
-
207
12 1994
-
THEORETICAL-STUDY OF AS2 DESORPTION FROM THE GA DANGLING-BOND SITE
Peer-reviewed
Y MOCHIZUKI, T TAKADA, C SASAOKA, A USUI, E MIYOSHI, Y SAKAI
PHYSICAL REVIEW B49
(
7
)
4658
-
4667
2 1994
-
THEORETICAL-STUDY OF THE CL DESORPTION REACTION INDUCED BY H-2 IN THE CHLORIDE ATOMIC LAYER EPITAXY
Peer-reviewed
Y MOCHIZUKI, T TAKADA, T SAKUMA, S HANDA, C SASAOKA, A USUI
JOURNAL OF CRYSTAL GROWTH135
(
1-2
)
259
-
268
1 1994
-
The combination of computational techniques such as computer graphics (CG), molecular dynamics (MD) and quantum chemistry (QC) methods are demonstrated to be effective for investigating the dynamics and formation of ordered metal species in zeolite pores.
Peer-reviewed
Mochizuki Y, Takada T, Usui A
Applied Surface Science82
(
83
)
543
1994
-
Theoretical Studies on the Dielectric Breakdown of the SiO_2 Thin Films
Peer-reviewed
YOKOZAWA Ayumi, OHTA Noriko, MOCHIZUKI Yuji, ISHITANI Akihiko, TAKADA Toshikazu
Science reports of the Research Institutes, Tohoku University. Ser. A, Physics, chemistry and metallurgy39
(
1
)
81
-
84
1994
-
THEORETICAL-STUDY OF THE GALLIUM CHLORIDE MOLECULE AND ITS INTERACTION WITH ARSENIC DANGLING BONDS
Peer-reviewed
Y MOCHIZUKI, T TAKADA, A USUI
PHYSICAL REVIEW B47
(
20
)
13420
-
13431
5 1993
-
NEW CONCERTED MECHANISM OF THE CL-REMOVAL REACTION INDUCED BY H-2 IN CHLORIDE ATOMIC LAYER EPITAXY
Peer-reviewed
Y MOCHIZUKI, T TAKADA, A USUI
JAPANESE JOURNAL OF APPLIED PHYSICS PART 2-LETTERS32
(
2A
)
L197
-
L199
2 1993
-
THEORETICAL-STUDIES ON THE ALE PROCESS OF GAAS CRYSTALS
Peer-reviewed
Y MOCHIZUKI, T TAKADA
NEC RESEARCH & DEVELOPMENT33
(
3
)
518
-
531
7 1992
-
ELECTRONIC-STRUCTURE OF LOWER SINGLET-STATES OF BINUCLEAR COPPER-ACETATE MONOHYDRATE
Peer-reviewed
K OGASAWARA, Y MOCHIZUKI, T NORO, K TANAKA
CANADIAN JOURNAL OF CHEMISTRY-REVUE CANADIENNE DE CHIMIE70
(
2
)
393
-
398
2 1992
-
A THEORETICAL-STUDY OF THE CUOH MOLECULE
Peer-reviewed
Y MOCHIZUKI, T TAKADA, A MURAKAMI
CHEMICAL PHYSICS LETTERS185
(
5-6
)
535
-
543
10 1991
-
ELECTRONIC-STRUCTURE OF THE LINEAR FORM OF OCUO
Peer-reviewed
Y MOCHIZUKI, K TANAKA, H KASHIWAGI
CHEMICAL PHYSICS151
(
1
)
11
-
20
3 1991
-
A THEORETICAL-STUDY OF THE BENT FORM OF CUO2
Peer-reviewed
Y MOCHIZUKI, U NAGASHIMA, S YAMAMOTO, H KASHIWAGI
CHEMICAL PHYSICS LETTERS164
(
2-3
)
225
-
230
12 1989
-
ELECTRONIC-STRUCTURE OF CO ADSORBED ON SMALL CU CLUSTERS - THEORETICAL-STUDY ON EXCITED-STATES
Peer-reviewed
Y MOCHIZUKI, K TANAKA, K OHNO, H TATEWAKI
PHYSICAL REVIEW B39
(
16
)
11907
-
11913
6 1989
-
ABINITIO CAS SCF/MRSDCI STUDY OF THE CUCH2 CLUSTER
Peer-reviewed
Y MOCHIZUKI, K TANAKA, K OHNO, H TATEWAKI, S YAMAMOTO
CHEMICAL PHYSICS LETTERS152
(
6
)
457
-
463
11 1988
-
Theoretical Study of the Electronic Structure of CO Adsorbed on Small Cu Clusters
Peer-reviewed
Tanaka K, Mochizuki Y, Kawaguchi T, Ohno K, Tatewaki H
Microclusters
82
1987
-
散逸粒子動力学(DPD)プログラムCAMUSの新規開発と性能評価
Peer-reviewed
土居英男, 齊藤天菜, 奥脇弘次, 内藤貴充, 望月祐志
J. Comp. Chem. Jpn.16
126
-
128
-
Structure-based drug designを指向した新規フラグメント分割法に基づく4体補正フラグメント分子軌道(FMO4)計算
渡邉千鶴, 福澤薫, 沖山佳生, 望月祐志, 塚本貴志, 加藤昭史, 田中成典, 中野達也
CBI学会誌1
42
-
46
-
AMOSSWEB: ab initio molecular orbital calculation service system in the world-wide web environment
Peer-reviewed
Mochizukia Yuji, Yamamotob Akinori, Hiraharab Yukio, Okamotob Naoki, Nishizawab Kaori, Okamotoa Yasuharu, Handab Susumu, Sakumab Toshihiro, Nakadab Hiroshi, Sanoa Tohru, o
-
Summary of this category
Peer-reviewed
Dumitrache A, Frunzulica F, Ionescu TC, c{C } }ekinmez Abdulkerim, Karaosmano{\u{g } }lu Bari{\c{s } }can, Erg{\"u}l, O}zg{\"u}r, Komeiji Yuto, Mochizuki Yuji, Nakano Tatsuya, Mori Hirotoshi