Docosahexaenoic acid enhances the treatment efficacy for castration-resistant prostate cancer by inhibiting autophagy through Atg4B inhibition.

Yudai Kudo, Kana Nakamura, Honoka Tsuzuki, Kotaro Hirota, Mina Kawai, Daisuke Takaya, Kaori Fukuzawa, Teruki Honma, Yuta Yoshino, Mitsuhiro Nakamura, Masaki Shiota, Naohiro Fujimoto, Akira Ikari, Satoshi Endo

Archives of biochemistry and biophysics　Vol. 760　p. 110135-110135　2024/08/23　Research paper (scientific journal)

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

2024/07/24

A machine learning model for predicting quantum chemistry based protein-drug molecule interactions

Ryosuke KITA, Chiduru WATANABE, Masateru OHTA, Naoki TANIMURA, Koji OKUWAKI, Mitsunori IKEGUCHI, Kaori FUKUZAWA, Teruki HONMA, Tsuyohiko FUJIGAYA, Koichiro KATO

The 38th Annual Conference of the Japanese Society for Artificial Intelligence　Vol. 38　2024/05　Research paper (international conference proceedings)

Characterization and drug solubilization of arginine-based ionic liquids – Impact of counterions and stoichiometry

Siran Wang, Qihui Xu, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi

International Journal of Pharmaceutics　p. 124228-124228　2024/05　Research paper (scientific journal)

Crystal Polymorph Search in the NPT Ensemble via a Deposition/Sublimation Alchemical Path

Aaron J. Nessler, Okimasa Okada, Yuya Kinoshita, Koki Nishimura, Hiroomi Nagata, Kaori Fukuzawa, Etsuo Yonemochi, Michael J. Schnieders

Crystal Growth & Design　2024/04/17　Research paper (scientific journal)

The Development and Characterization of Novel Ionic Liquids Based on Mono- and Dicarboxylates with Meglumine for Drug Solubilizers and Skin Permeation Enhancers

Takayuki Furuishi, Sara Taguchi, Siran Wang, Kaori Fukuzawa, Etsuo Yonemochi

Pharmaceutics　Vol. 16　No. 3　p. 322-322　2024/02/26　Research paper (scientific journal)

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

2024/02/08

Analysis of Moisture Stability in Amorphous Solid DispersionsUsing Molecular Dynamics and FMO Methods

Honoka MATSUMOTO, Koji OKUWAKI, Kenjirou HIGASHI, Takayuki FURUISHI, Kaori FUKUZAWA, Etsuo YONEMOCHI

Journal of Computer Chemistry, Japan　Vol. 23　No. 4　p. 115-125　2024　Research paper (scientific journal)

Probing RNA–Small Molecule Interactions Using Biophysical and Computational Approaches

Amiu Shino, Maina Otsu, Koji Imai, Kaori Fukuzawa, Ella Czarina Morishita

ACS Chemical Biology　2023/11/17　Research paper (scientific journal)

Pateamine A mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs

Shintaro Iwasaki, Hironori Saito, Yuma Handa, Mingming Chen, Tilman Schneider-Poetsch, Yuichi Shichino, Mari Takahashi, Daniel Romo, Minoru Yoshida, Alois Furstner, Takuhiro Ito, Kaori Fukuzawa

2023/09/21

Crystal structure prediction with force field, DFT-D3 and FMO techniques

S. Obata, Y. Utsumi, Y. Ikabata, K. Okuwaki, K. Fukuzawa, N. Nakayama, E. Yonemochi, H. Goto

Acta Crystallographica Section A Foundations and Advances　Vol. 79　No. a2　p. C890-C890　2023/08/22　Research paper (scientific journal)

Prediction of Binding Pose and Affinity of SARS-CoV-2 Main Protease and Repositioned Drugs by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations

Yuma Handa, Koji Okuwaki, Yusuke Kawashima, Ryo Hatada, Yuji Mochizuki, Yuto Komeiji, Shigenori Tanaka, Takayuki Furuishi, Etsuo Yonemochi, Teruki Honma, Kaori Fukuzawa

2023/07/25

Application of Model Core Potentials to Zn- and Mg-containing Metalloproteins in the Fragment Molecular Orbital Method

Koichiro Kato*, Ami Yamamoto, Chiduru Watanabe, Kaori Fukuzawa

Chem-Bio Informatics Journal　Vol. 23　p. 14-25　2023/07/20　Research paper (scientific journal)

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

Journal of Chemical Information and Modeling　2023/07/12　Research paper (scientific journal)

Characterization of Co-amorphous Carvedilol–Maleic Acid System Prepared by Solvent Evaporation

Takayuki Furuishi, Nanami Sato-Hata, Kaori Fukuzawa, Etsuo Yonemochi

Pharmaceutical Development and Technology　p. 1-13　2023/03/22　Research paper (scientific journal)

Functional molecular evolution of a GTP sensing kinase: PI5P4Kβ.

Koh Takeuchi, Miki Senda, Yoshiki Ikeda, Koji Okuwaki, Kaori Fukuzawa, So Nakagawa, Mika Sasaki, Atsuo T Sasaki, Toshiya Senda

The FEBS journal　2023/03/01　Research paper (scientific journal)

Structure and Mechanism Analysis of Proteins by Fragment Molecular Orbital Calculations

Kaori FUKUZAWA, Chiduru WATANABE, Koichiro KATO

Nihon Kessho Gakkaishi　Vol. 65　No. 1　p. 17-25　2023/02/28　Research paper (scientific journal)

Promoting Activity of Terpenes on Skin Permeation of Famotidine

Qihui Xu, Yifan Wu, Hiroki Saito, Yuki Ofuchi, Haruna Setoyama, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi, Yasuko Obata

Chemical and Pharmaceutical Bulletin　Vol. 71　No. 2　p. 111-119　2023/02/01　Research paper (scientific journal)

Physicochemical Properties and Transdermal Absorption of a Flurbiprofen and Lidocaine Complex in the Non-Crystalline Form

Qihui Xu, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi

Pharmaceutics　Vol. 15　No. 2　2023/01　Research paper (scientific journal)

Quantum Chemical Interaction Analysis between SARS-CoV-2 Main Protease and Ensitrelvir (Xocova) Compared with Its Initial Screening Hit

Chiduru Watanabe, Shigenori Tanaka, Yoshio Okiyama, Hitomi Yuki, Tatsuya Ohyama, Kikuko Kamisaka, Daisuke Takaya, Kaori Fukuzawa, Teruki Honma

2022/12/02　Research paper (scientific journal)

Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti

Kazue Inaba, Kana Ebihara, Miki Senda, Ryunosuke Yoshino, Chisako Sakuma, Kotaro Koiwai, Daisuke Takaya, Chiduru Watanabe, Akira Watanabe, Yusuke Kawashima, Kaori Fukuzawa, Riyo Imamura, Hirotatsu Kojima, Takayoshi Okabe, Nozomi Uemura, Shinji Kasai, Hirotaka Kanuka, Takashi Nishimura, Kodai Watanabe, Hideshi Inoue, Yuuta Fujikawa, Teruki Honma, Takatsugu Hirokawa, Toshiya Senda, Ryusuke Niwa

BMC Biology　Vol. 20　No. 1　2022/12　Research paper (scientific journal)

Fragment molecular orbital calculations containing Mg<sup>2+</sup> ions: PPlase domain of Cyclophilin G

Masayasu Fujii, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka

Chem-Bio Informatics Journal　Vol. 22　p. 55-62　2022/09/16　Research paper (scientific journal)

Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives.

Chiaki Handa, Yuki Yamazaki, Shigeru Yonekubo, Noritaka Furuya, Takaki Momose, Tomonaga Ozawa, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi

The Journal of steroid biochemistry and molecular biology　Vol. 222　p. 106152-106152　2022/09　Research paper (scientific journal)

Study of Orally Disintegrating Tablets Using Erythritol as an Excipient Produced by Moisture-Activated Dry Granulation (MADG)

Mizuki Yamada, Agata Ishikawa, Shun Muramatsu, Takayuki Furuishi, Yoshinori Onuki, Kaori Fukuzawa, Etsuo Yonemochi

Pharmaceuticals　Vol. 15　No. 8　p. 1004-1004　2022/08/15　Research paper (scientific journal)

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, Kaori Fukuzawa, Shigenori Tanaka

Journal of Computational Chemistry　Vol. 43　No. 20　p. 1362-1371　2022/07/30　Research paper (scientific journal)

The GTP responsiveness of PI5P4Kβ evolved from a compromised trade-off between activity and specificity.

Koh Takeuchi, Yoshiki Ikeda, Miki Senda, Ayaka Harada, Koji Okuwaki, Kaori Fukuzawa, So Nakagawa, Hong Yang Yu, Lisa Nagase, Misaki Imai, Mika Sasaki, Yu-Hua Lo, Doshun Ito, Natsuki Osaka, Yuki Fujii, Atsuo T Sasaki, Toshiya Senda

Structure (London, England : 1993)　Vol. 30　No. 6　p. 886-899　2022/06/02　Research paper (scientific journal)

FMO calculations for zinc metalloprotease: Fragmentation of amino-acid residues coordinated to zinc ion

Imai, K., Takimoto, D., Saito, R., Watanabe, C., Fukuzawa, K., Kurita, N.

Chem-Bio Informatics Journal　Vol. 22　p. 21-25　2022/06　Research paper (scientific journal)

Computational approach to elucidate the formation and stabilization mechanism of amorphous formulation using molecular dynamics simulation and fragment molecular orbital calculation.

Xiaohan Ma, Kenjirou Higashi, Kaori Fukuzawa, Keisuke Ueda, Kazunori Kadota, Yuichi Tozuka, Etsuo Yonemochi, Kunikazu Moribe

International journal of pharmaceutics　Vol. 615　p. 121477-121477　2022/03/05　Research paper (scientific journal)

Fragment molecular orbital calculations for biomolecules

Fukuzawa, K., Tanaka, S.

Current Opinion in Structural Biology　Vol. 72　p. 127-134　2022/02　Research paper (scientific journal)

Sulfated Hyaluronan Binds to Heparanase and Blocks Its Enzymatic and Cellular Actions in Carcinoma Cells

Shi, J., Kanoya, R., Tani, Y., Ishikawa, S., Maeda, R., Suzuki, S., Kawanami, F., Miyagawa, N., Takahashi, K., Oku, T., Yamamoto, A., Fukuzawa, K., Nakajima, M., Irimura, T., Higashi, N.

International Journal of Molecular Sciences　Vol. 23　No. 9　2022　Research paper (scientific journal)

Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method

Koji Okuwaki, Kazuki Akisawa, Ryo Hatada, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka

Applied Physics Express　Vol. 15　No. 1　p. 017001-017001　2022/01/01　Research paper (scientific journal)

Altered Media Flow and Tablet Position as Factors of How Air Bubbles Affect Dissolution of Disintegrating and Non-disintegrating Tablets Using a USP 4 Flow-Through Cell Apparatus

Hiroyuki Yoshida, Keita Teruya, Yasuhiro Abe, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi, Ken-ichi Izutsu

AAPS PHARMSCITECH　Vol. 22　No. 7　2021/08　Research paper (scientific journal)

Dynamic Cooperativity of Ligand–Residue Interactions Evaluated with the Fragment Molecular Orbital Method

Shigenori Tanaka, Shusuke Tokutomi, Ryo Hatada, Koji Okuwaki, Kazuki Akisawa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki

The Journal of Physical Chemistry B　Vol. 125　No. 24　p. 6501-6512　2021/06/24　Research paper (scientific journal)

Special feature of COVID-19 in 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, Tatsuya Ohyama, Kikuko Kamisaka, Daisuke Takaya, Teruki Honma

2021/06/18

Computational ab initio interaction analyses between neutralizing antibody and SARS-CoV-2 variant spike proteins using the fragment molecular orbital method

Kazuki Watanabe, Chiduru Watanabe, Teruki Honma, Yu-Shi Tian, Yusuke Kawashima, Norihito Kawashita, Kaori Fukuzawa, Tatsuya Takagi

Bulletin of the Chemical Society of Japan　2021/05/15　Research paper (scientific journal)

Manufacturability and Properties of Granules and Tablets Using the Eco-Friendly Granulation Method Green Fluidized Bed Granulation Compared to Direct Compression

Agata Ishikawa, Hiroshi Takasaki, Atsushi Sakurai, Takuma Katayama, Koichi Wada, Takayuki Furuishi, Kaori Fukuzawa, Yasuko Obata, Etsuo Yonemochi

Chemical and Pharmaceutical Bulletin　Vol. 69　No. 5　p. 447-455　2021/05/01　Research paper (scientific journal)

Stabilization mechanism of amorphous carbamazepine by transglycosylated rutin, a non-polymeric amorphous additive with a high glass transition temperature.

Chisa Aoki, Xiaohan Ma, Kenjirou Higashi, Yuya Ishizuka, Keisuke Ueda, Kazunori Kadota, Kaori Fukuzawa, Yuichi Tozuka, Kohsaku Kawakami, Etsuo Yonemochi, Kunikazu Moribe

International journal of pharmaceutics　Vol. 600　p. 120491-120491　2021/05/01　Research paper (scientific journal)

Intermolecular Interaction Analyses on SARS-CoV-2 Spike Protein Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/Peptide Using Fragment Molecular Orbital Calculation

Kazuki Watanabe, Chiduru Watanabe, Teruki Honma, Yu-Shi Tian, Yusuke Kawashima, Norihito Kawashita, Tatsuya Takagi, Kaori Fukuzawa

The Journal of Physical Chemistry Letters　Vol. 12　No. 16　p. 4059-4066　2021/04/29　Research paper (scientific journal)

Crystal Structures of Antiarrhythmic Drug Disopyramide and Its Salt with Phthalic Acid

Majid Ismail Tamboli, Yushi Okamoto, Yohei Utsumi, Takayuki Furuishi, Siran Wang, Daiki Umeda, Okky Dwichandra Putra, Kaori Fukuzawa, Hidehiro Uekusa, Etsuo Yonemochi

Crystals　Vol. 11　No. 4　p. 379-379　2021/04/06　Research paper (scientific journal)

Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses dagger

Chiduru Watanabe, Yoshio Okiyama, Shigenori Tanaka, Kaori Fukuzawa, Teruki Honma

CHEMICAL SCIENCE　Vol. 12　No. 13　2021/04　Research paper (scientific journal)

Crystal Structure of Novel Terephthalate Salt of Antiarrhythmic Drug Disopyramide

Majid Ismail Tamboli, Yohei Utusmi, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi

Crystals　Vol. 11　No. 4　2021/03/31　Research paper (scientific journal)

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, Kenichiro Takaba, Tomonaga Ozawa, Midori Takimoto-Kamimura, Shigenori Tanaka, Kaori Fukuzawa, Teruki Honma

Journal of Chemical Information and Modeling　Vol. 61　No. 2　p. 777-794　2021/02/22　Research paper (scientific journal)

Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation

Ryo Hatada, Koji Okuwaki, Kazuki Akisawa, Yuji Mochizuki, Yuma Handa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka

Applied Physics Express　Vol. 14　No. 2　p. 027003-027003　2021/02/01　Research paper (scientific journal)

Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital (FMO) Method

Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuto Komeiji, Katsunori Segawa, Yuji Mochizuki

Bulletin of the Chemical Society of Japan　Vol. 94　No. 1　p. 91-96　2021/01/15　Research paper (scientific journal)

FMO Drug Design Consortium

Fukuzawa, K., Tanaka, S., Yagi, Y., Kurita, N., Kawashita, N., Takaba, K., Honma, T.

Recent Advances of the Fragment Molecular Orbital Method: Enhanced Performance and Applicability　2021　Research paper (scientific journal)

Improving the Accuracy of Crystal Structure Prediction Using FMO Crystal Energy: An Example of Target XXIII

Yohei UTSUMI, Daiki UMEDA, Koji OKUWAKI, Shigeaki OBATA, Naofumi NAKAYAMA, Hitoshi GOTO, Takayuki FURUISHI, Kaori FUKUZAWA, Etsuo YONEMOCHI

Journal of Computer Chemistry, Japan　Vol. 20　No. 3　p. 92-93　2021　Research paper (scientific journal)

Estimation of Graph Convolutional Network in Ames Prediction of Drug Candidate Compounds

HANDA Chiaki, OZAWA Tomonaga, FUKUZAWA Kaori, YONEMOCHI Etsuo

Journal of Computer Chemistry, Japan　Vol. 20　No. 1　p. 1-9　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　p. 407-424　2021　Part of collection (book)

The ABINIT-MP Program

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　p. 53-67　2021　Part of collection (book)

How to Perform FMO Calculation in Drug Discovery

Kaori Fukuzawa, Chiduru Watanabe, Yoshio Okiyama, Tatsuya Nakano

Recent Advances of the Fragment Molecular Orbital Method　p. 93-125　2021　Part of collection (book)

Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations

Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka

RSC Advances　Vol. 11　No. 6　p. 3272-3279　2021　Research paper (scientific journal)

Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method

Shigenori Tanaka, Chiduru Watanabe, Teruki Honma, Kaori Fukuzawa, Kazue Ohishi, Tadashi Maruyama

Journal of Molecular Graphics and Modelling　Vol. 100　p. 107650-107650　2020/11　Research paper (scientific journal)

Intermolecular interaction among Remdesivir, RNA and RNA-dependent RNA polymerase of SARS-CoV-2 analyzed by fragment molecular orbital calculation

Kato, K., Honma, T., Fukuzawa, K.

Journal of Molecular Graphics and Modelling　Vol. 100　p. 107695-107695　2020/11　Research paper (scientific journal)

Machine learning prediction of inter-fragment interaction energies between ligand and amino-acid residues on the fragment molecular orbital calculations for Janus kinase - inhibitor complex

Shusuke Tokutomi, Kohei Shimamura, Kaori Fukuzawa, Shigenori Tanaka

CHEMICAL PHYSICS LETTERS　Vol. 757　2020/10　Research paper (scientific journal)

Self-Degradable Lipid-Like Materials Based on "Hydrolysis accelerated by the intra-Particle Enrichment of Reactant (HyPER)" for Messenger RNA Delivery

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 MATERIALS　Vol. 30　No. 34　2020/08　Research paper (scientific journal)

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, Masateru Ohta, Mitsunori Ikeguchi, Yasushi Okuno, Kaori Fukuzawa, Teruki Honma

Journal of Chemical Information and Modeling　Vol. 60　No. 7　p. 3361-3368　2020/07/27　Research paper (scientific journal)

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

Journal of Chemical Information and Modeling　Vol. 60　No. 7　p. 3593-3602　2020/07/27　Research paper (scientific journal)

Activity-specificity trade-off gives PI5P4Kβ a nucleotide preference to function as a GTP-sensing kinase

Koh Takeuchi, Yoshiki Ikeda, Miki Senda, Ayaka Harada, Koji Okuwaki, Kaori Fukuzawa, So Nakagawa, Hongyang Yu, Lisa Nagase, Misaki Imai, Mika Sasaki, YuHua Lo, Atsuo T. Sasaki, Toshiya Senda

2020/06/10

Fragmentation at sp2 carbon atoms in fragment molecular orbital method

Yoshinobu Akinaga, Koichiro Kato, Tatsuya Nakano, Kaori Fukuzawa, Yuji Mochizuki

Journal of Computational Chemistry　Vol. 41　No. 15　p. 1416-1420　2020/06/05　Research paper (scientific journal)

An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo

Kotaro Koiwai, Kazue Inaba, Kana Morohashi, Sora Enya, Reina Arai, Hirotatsu Kojima, Takayoshi Okabe, Yuuta Fujikawa, Hideshi Inoue, Ryunosuke Yoshino, Takatsugu Hirokawa, Koichiro Kato, Kaori Fukuzawa, Yuko Shimada-Niwa, Akira Nakamura, Fumiaki Yumoto, Toshiya Senda, Ryusuke Niwa

JOURNAL OF BIOLOGICAL CHEMISTRY　Vol. 295　No. 20　p. 7154-7167　2020/05　Research paper (scientific journal)

Crystal Structural Analysis of DL-Mandelate Salt of Carvedilol and Its Correlation with Physicochemical Properties

Nanami Hata, Takayuki Furuishi, Majid I. Tamboli, Momiji Ishizaki, Daiki Umeda, Kaori Fukuzawa, Etsuo Yonemochi

Crystals　2020/01/20　Research paper (scientific journal)

Development Status of ABINIT-MP in 2020

Yuji MOCHIZUKI, Kota SAKAKURA, Hiromasa WATANABE, Koji OKUWAKI, Koichiro KATO, Naoki WATANABE, Yoshio OKIYAMA, Kaori FUKUZAWA, Tatsuya NAKANO

Journal of Computer Chemistry, Japan　Vol. 19　No. 4　p. 142-145　2020　Research paper (scientific journal)

Interaction Analyses between Calcite/Apatite and Peptides by Fragment Molecular Orbital Method

Ryo HATADA, Kouichiro KATO, Koji OKUWAKI, Kaori FUKUZAWA, Yuji MOCHIZUKI

Journal of Computer Chemistry, Japan　Vol. 19　No. 1　p. 1-7　2020　Research paper (scientific journal)

Folding simulation of small proteins by dissipative particle dynamics (DPD) with non-empirical interaction parameters based on fragment molecular orbital calculations

Koji Okuwaki, Hideo Doi, Kaori Fukuzawa, Yuji Mochizuki

Applied Physics Express　Vol. 13　No. 1　p. 017002-017002　2020/01/01　Research paper (scientific journal)

Interaction between calcite and adsorptive peptide analyzed by fragment molecular orbital method

Koichiro Kato, Kaori Fukuzawa, Yuji Mochizuki

Japanese Journal of Applied Physics　Vol. 58　No. 12　p. 120906-120906　2019/12/01　Research paper (scientific journal)

Crystal structure prediction of irsogladine maleate by experimental and computational methods

Chinatsu Sakata, Yushi Okamoto, Daiki Umeda, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi

J. Comput. Chem. Jpn　Vol. 18　p. 156-158　2019/11　Research paper (scientific journal)

Effect of sulfobutyl ether-β-cyclodextrin and propylene glycol alginate on the solubility of clozapine

Takayuki Furuishi, Kohei Sekino, Mihoko Gunji, Kaori Fukuzawa, Hiromasa Nagase, Tomohiro Endo, Haruhisa Ueda, Etsuo Yonemochi

Pharmaceutical Development and Technology　Vol. 24　No. 4　p. 479-486　2019/04　Research paper (scientific journal)

Development of an automated fragment molecular orbital (FMO) calculation protocol toward construction of quantum mechanical calculation database for large biomolecules

Chiduru Watanabe, Hirofumi Watanabe, Yoshio Okiyama, Daisuke Takaya, Kaori Fukuzawa, Shigenori Tanaka, Teruki Honma

Chem-Bio Informatics Journal　Vol. 19　No. 0　p. 5-18　2019/03　Research paper (scientific journal)

The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA.

Shintaro Iwasaki, Wakana Iwasaki, Mari Takahashi, Ayako Sakamoto, Chiduru Watanabe, Yuichi Shichino, Stephen N Floor, Koichi Fujiwara, Mari Mito, Kosuke Dodo, Mikiko Sodeoka, Hiroaki Imataka, Teruki Honma, Kaori Fukuzawa, Takuhiro Ito, Nicholas T Ingolia

Molecular cell　Vol. 73　No. 4　p. 738-748　2019/02/21　Research paper (scientific journal)

Destabilization of DNA through interstrand crosslinking by UO₂²⁺

Rossberg, A., Abe, T., Okuwaki, K., Barkleit, A., Fukuzawa, K., Nakano, T., Mochizuki, Y., Tsushima, S.

Chemical Communications　Vol. 55　No. 14　p. 2015-2018　2019/02/18　Research paper (scientific journal)

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

Yoshio Okiyama, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

The Journal of Physical Chemistry B　Vol. 123　No. 5　p. 957-973　2019/02/07　Research paper (scientific journal)

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, Vladimir Sladek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu, Yasuteru Shigeta

Journal of Chemical Information and Modeling　Vol. 59　No. 1　p. 25-30　2019/01/28　Research paper (scientific journal)

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

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.　Vol. 17　No. 4　p. 172-179　2019/01

A Radical Correction for Inter Fragment Interaction Energy (IFIE) between Fragments Sharing Bond Detached Atom (BDA)

Tatsuya Nakano, Yuji Mochidzuki, Kaori Fukuzawa, Yoshio Okiyama, Chiduru Watanabe

Journal of Computer Aided Chemistry　Vol. 20　No. 0　p. 1-6　2019　Research paper (scientific journal)

Development of an automated fragment molecular orbital (FMO) calculation protocol toward construction of quantum mechanical calculation database for large biomolecules

Chiduru Watanabe, Hirofumi Watanabe, Yoshio Okiyama, Daisuke Takaya, Kaori Fukuzawa, Shigenori Tanaka, Teruki Honma

CHEM-BIO INFORMATICS JOURNAL　Vol. 19　p. 5-18　2019　Research paper (scientific journal)

Interaction between a Single-Stranded DNA and a Binding Protein Viewed by the Fragment Molecular Orbital Method

Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa

Bulletin of the Chemical Society of Japan　Vol. 91　No. 11　p. 1596-1605　2018/11　Research paper (scientific journal)

Application of singular value decomposition to the inter-fragment interaction energy analysis for ligand screening

Keiya Maruyama, Yinglei Sheng, Hirofumi Watanabe, Kaori Fukuzawa, Shigenori Tanaka

Computational and Theoretical Chemistry　Vol. 1132　p. 23-34　2018/05/15　Research paper (scientific journal)

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

Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka

The Journal of Physical Chemistry B　Vol. 122　No. 16　p. 4457-4471　2018/04/26　Research paper (scientific journal)

Development and Application of FMO Calculation − DPD Simulation Conbination Scheme

Okuwaki Koji, Doi Hideo, Mochizuki Yuji, Ozawa Taku, Yasuoka Kenji, Fukuzawa Kaori

Journal of Computer Chemistry, Japan　Vol. 17　No. 3　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

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.　Vol. 17　p. 144-146　2018

Formation Mechanism of Lipid Membrane and Vesicle Using Small Angle X-ray Scattering and Dissipative Particle Dynamics (DPD) Method

Eiji Shinsho, Koji Okuwaki, Hideo Doi, Yuji Mochizuki, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi

JOURNAL OF COMPUTER CHEMISTRY-JAPAN　Vol. 17　No. 4　p. 172-179　2018　Research paper (scientific journal)

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

Yinglei Sheng, Hirofumi Watanabe, Keiya Maruyama, Chiduru Watanabe, Yoshio Okiyama, Teruki Honma, Kaori Fukuzawa, Shigenori Tanaka

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL　Vol. 16　p. 421-434　2018　Research paper (scientific journal)

Analysis of ligand binding specificity of estrogen receptor by the fragment molecular orbital method

Yuya Seki, Tsukasa Kato, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yone

JOURNAL OF COMPUTER CHEMISTRY-JAPAN　Vol. 17　No. 3　p. 160-162　2018　Research paper (scientific journal)

Accuracy of Dimer-ES Approximation on Fragment Molecular Orbital (FMO) Method

Nakano Tatsuya, Fukuzawa Kaori, Okiyama Yoshio, Watanabe Chiduru, Komeiji Yuto, Mochizuki Yuji

CHEM-BIO INFORMATICS JOURNAL　Vol. 18　p. 119-122　2018　Research paper (scientific journal)

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

Chiduru Watanabe, Hirofumi Watanabe, Kaori Fukuzawa, Lorien J. Parker, Yoshio Okiyama, Hitomi Yuki, Shigeyuki Yokoyama, Hirofumi Nakano, Shigenori Tanaka, Teruki Honma

JOURNAL OF CHEMICAL INFORMATION AND MODELING　Vol. 57　No. 12　p. 2996-3010　2017/12　Research paper (scientific journal)

Epalrestat tetrahydrofuran monosolvate: crystal structure and phase transition

Daiki Umeda, Okky Dwichandra Putra, Mihoko Gunji, Kaori Fukuzawa, Etsuo Yonemochi

ACTA CRYSTALLOGRAPHICA SECTION E-CRYSTALLOGRAPHIC COMMUNICATIONS　Vol. 73　p. 941-+　2017/07　Research paper (scientific journal)

Solubility improvement of epalrestat by layered structure formation via cocrystallization

Okky Dwichandra Putra, Daiki Umeda, Yuda Prasetya Nugraha, Takayuki Furuishi, Hiromasa Nagase, Kaori Fukuzawa, Hidehiro Uekusa, Etsuo Yonemochi

CRYSTENGCOMM　Vol. 19　No. 19　p. 2614-2622　2017/05　Research paper (scientific journal)

Fragment molecular orbital (FMO) calculations on DNA by a scaled third-order Moller-Plesset perturbation (MP2.5) scheme

Haruka Yamada, Yuji Mochizuki, Kaori Fukuzawa, Yoshio Okiyama, Yuto Komeiji

COMPUTATIONAL AND THEORETICAL CHEMISTRY　Vol. 1101　p. 46-54　2017/02　Research paper (scientific journal)

Explicit solvation of a single-stranded DNA, a binding protein, and their complex: A suitable protocol for fragment molecular orbital calculation

Komeiji, Y., Okiyama, Y., Mochizuki, Y., Fukuzawa, K.

Chem-Bio Informatics Journal　Vol. 17　No. 0　p. 72-84　2017　Research paper (scientific journal)

Current Status of ABINIT-MP as a FMO Program and Related Works with Machine Learning

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, Japan　Vol. 16　No. 5　p. 119-122　2017　Research paper (scientific journal)

FMOプログラムABINIT-MPの開発状況と機械学習との連携

望月祐志, 坂倉耕太, 秋永宜伸, 加藤幸一郎, 渡邊啓正, 沖山佳生, 中野達也, 古明地勇人, 奥沢明, 福澤薫, 田中成典

J. Comp. Chem. Jpn.　Vol. 16　p. 119-122　2017

A new solvate of epalerstat, a drug for diabetic neuropathy

Okky Dwichandra Putra, Daiki Umeda, Kaori Fukuzawa, Mihoko Gunji, Etsuo Yonemochi

Acta Crystallographica Section E: Crystallographic Communications　Vol. 73　p. 1264-1267　2017　Research paper (scientific journal)

Explicit solvation of a single-stranded DNA, a binding protein, and their complex: a suitable protocol for fragment molecular orbital calculation

Komeiji Yuto, Okiyama Yoshio, Mochizuki Yuji, Fukuzawa Kaori

CHEM-BIO INFORMATICS JOURNAL　Vol. 17　p. 72-84　2017

A Preliminary Study of Correction for Inter Fragment Interaction Energy (IFIE) between Fragments Sharing Bond Detached Atom (BDA)

Tatsuya Nakano, Yuji Mochidzuki, Kaori Fukuzawa, Yoshio Okiyama, Chiduru Watanabe

Journal of Computer Aided Chemistry　Vol. 18　No. 0　p. 143-148　2017　Research paper (scientific journal)

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

Kana Tokuda, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji

JOURNAL OF MOLECULAR GRAPHICS & MODELLING　Vol. 69　p. 144-153　2016/09　Research paper (scientific journal)

Fragment Molecular Orbital (FMO) Calculations of Peptoids

KAWADA Shutaro, SAKAGUCHI Masataka, YONEKURA Ibuki, OKUWAKI Kouji, MOCHIZUKI Yuji, FUKUZAWA Kaori

Journal of Computer Chemistry, Japan　Vol. 15　No. 3　p. 51-52　2016

Effects of Water Molecules and Configurations of Neighboring Amino Acid Residues Surrounding DsRed Chromophore on Its Excitation Energy

Masataka SAKAGUCHI, Yuji MOCHIZUKI, Chiduru WATANABE, Kaori FUKUZAWA

Journal of Computer Chemistry, Japan　Vol. 14　No. 5　p. 155-163　2015/12/03　Research paper (scientific journal)

Novel type of virtual ligand screening on the basis of quantum-chemical calculations for protein-ligand complexes and extended clustering techniques

Ryo Kurauchi, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka

COMPUTATIONAL AND THEORETICAL CHEMISTRY　Vol. 1061　p. 12-22　2015/06　Research paper (scientific journal)

Modeling of hydroxyapatite-peptide interaction based on fragment molecular orbital method

Koichiro Kato, Kaori Fukuzawa, Yuji Mochizuki

CHEMICAL PHYSICS LETTERS　Vol. 629　p. 58-64　2015/06　Research paper (scientific journal)

Explicit solvation modulates intra- and inter-molecular interactions within DNA: Electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method

Kaori Fukuzawa, Ikuo Kurisaki, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Shigenori Tanaka, Yuto Komeiji

Computational and Theoretical Chemistry　Vol. 1054　p. 29-37　2015/02　Research paper (scientific journal)

Implementation of Pair Interaction Energy DecompositionAnalysis and Its Applications to Protein-Ligand Systems

Takayuki TSUKAMOTO, Koichiro KATO, Akifumi KATO, Tatsuya NAKANO, Yuji MOCHIZUKI, Kaori FUKUZAWA

Journal of Computer Chemistry, Japan　Vol. 14　No. 1　p. 1-9　2015　Research paper (scientific journal)

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

Shinji Amari, Yuji Mochizuki, Akifumi Kato, Kaori Fukuzawa, Chiduru Watanabe, Yoshio Okiyama, Tatsuya Nakano

Vol. 2　No. 4　p. 17-25　2014/11/30　Research paper (bulletin of university, research institution)

インシリコ創薬におけるFMO法と周辺基盤技術の進歩

福澤薫

SAR News No.27　2014/10　Research paper (scientific journal)

Interaction energy analysis on specific binding of influenza virus hemagglutinin to avian and human sialosaccharide receptors: Importance of mutation-induced structural change

Satoshi Anzaki, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka

JOURNAL OF MOLECULAR GRAPHICS & MODELLING　Vol. 53　p. 48-58　2014/09　Research paper (scientific journal)

Charge Clamps of Lysines and Hydrogen Bonds Play Key Roles in the Mechanism to Fix Helix 12 in the Agonist and Antagonist Positions of Estrogen Receptor alpha: Intramolecular Interactions Studied by the Ab Initio Fragment Molecular Orbital Method

Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka, Sachiko Aida-Hyugaji

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 118　No. 19　p. 4993-5008　2014/05　Research paper (scientific journal)

Accuracy of the fragment molecular orbital (FMO) calculations for DNA: Total energy, molecular orbital, and inter-fragment interaction energy

Kaori Fukuzawa, Chiduru Watanabe, Ikuo Kurisaki, Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka, Yuto Komeiji

COMPUTATIONAL AND THEORETICAL CHEMISTRY　Vol. 1034　p. 7-16　2014/04　Research paper (scientific journal)

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

Shigenori Tanaka, Yuji Mochizuki, Yuto Komeiji, Yoshio Okiyama, Kaori Fukuzawa

PHYSICAL CHEMISTRY CHEMICAL PHYSICS　Vol. 16　No. 22　p. 10310-10344　2014　Research paper (scientific journal)

Modeling of peptide–silica interaction based on four-body corrected fragment molecular orbital (FMO4) calculations

Yoshio Okiyama, Takayuki Tsukamoto, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka, Yuji Mochizuki

Chemical Physics Letters　Vol. 566　p. 25-31　2013/04　Research paper (scientific journal)

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

Chiduru Watanabe, Kaori Fukuzawa, Yoshio Okiyama, Takayuki Tsukamoto, Akifumi Kato, Shigenori Tanaka, Yuji Mochizuki, Tatsuya Nakano

JOURNAL OF MOLECULAR GRAPHICS & MODELLING　Vol. 41　p. 31-42　2013/04　Research paper (scientific journal)

Device, system, method and program for producing fragment model

Mochizuki Yuji, Tsukamoto Takayuki, Fukuzawa Kaori

2013/03

ABINIT-MP/BioStation によるFMO 法の創薬への適用

福澤薫, 渡邉千鶴

CICSJ Bulletin　Vol. 31　No. 4　p. 89-89　2013　Research paper (scientific journal)

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　2013　Research paper (scientific journal)

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　Vol. 1　No. 1　2013　Research paper (scientific journal)

Interaction energy calculation system, method and program

Nakano Tatsuya, Mochizuki Yuji, Fukuzawa Kaori

2012/08

Partial geometry optimization with FMO-MP2 gradient: Application to TrpCage

Takayuki Tsukamoto, Yuji Mochizuki, Naoki Watanabe, Kaori Fukuzawa, Tatsuya Nakano

CHEMICAL PHYSICS LETTERS　Vol. 535　p. 157-162　2012/05　Research paper (scientific journal)

New fragmentation of fragment molecular orbital method applicable to fragment based drug design

Watanabe Chiduru, Fukuzawa Kaori, Okiyama Yoshio, Tsukamoto Takayuki, Kato Akifumi, Tanaka Shigenori, Nakano Tatsuya, Mochizuki Yuji

2012

Continuous multipole methodによるfragment molecular orbital法の高速化

中野達也, 山下勝美, 瀬川勝智, 沖山佳生, 渡邊千鶴, 福澤薫, 田中成典, 望月祐志

p. 44-50　2012

Development of the four-body corrected fragment molecular orbital (FMO4) method

Tatsuya Nakano, Yuji Mochizuki, Katsumi Yamashita, Chiduru Watanabe, Kaori Fukuzawa, Katsunori Segawa, Yoshio Okiyama, Takayuki Tsukamoto, Shigenori Tanaka

Chemical Physics Letters　Vol. 523　p. 128-133　2012/01　Research paper (scientific journal)

Antigen-antibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation

Akio Yoshioka, Kazutomo Takematsu, Ikuo Kurisaki, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Eri Nobusawa, Katsuhisa Nakajima, Shigenori Tanaka

THEORETICAL CHEMISTRY ACCOUNTS　Vol. 130　No. 4-6　p. 1197-1202　2011/12　Research paper (scientific journal)

Higher-order correlated calculations based on fragment molecular orbital scheme

Yuji Mochizuki, Katsumi Yamashita, Tatsuya Nakano, Yoshio Okiyama, Kaori Fukuzawa, Naoki Taguchi, Shigenori Tanaka

THEORETICAL CHEMISTRY ACCOUNTS　Vol. 130　No. 2-3　p. 515-530　2011/10　Research paper (scientific journal)

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

Akio Yoshioka, Kaori Fukuzawa, Yuji Mochizuki, Katsumi Yamashita, Tatsuya Nakano, Yoshio Okiyama, Eri Nobusawa, Katsuhisa Nakajima, Shigenori Tanaka

JOURNAL OF MOLECULAR GRAPHICS & MODELLING　Vol. 30　p. 110-119　2011/09　Research paper (scientific journal)

Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme

Yoshio Okiyama, Kaori Fukuzawa, Haruka Yamada, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

Chemical Physics Letters　Vol. 509　No. 1-3　p. 67-71　2011/06　Research paper (scientific journal)

Sialic Acid Recognition of the Pandemic Influenza 2009 H1N1 Virus: Binding Mechanism Between Human Receptor and Influenza Hemagglutinin

Kaori Fukuzawa, Katsumi Omagari, Katsuhisa Nakajima, Eri Nobusawa, Shigenori Tanaka

PROTEIN AND PEPTIDE LETTERS　Vol. 18　No. 5　p. 530-539　2011/05　Research paper (scientific journal)

Fragment molecular orbital (FMO) study on stabilization mechanism of neuro-oncological ventral antigen (NOVA)-RNA complex system

Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM　Vol. 962　No. 1-3　p. 45-55　2010/12　Research paper (scientific journal)

Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA)

Yuji Mochizuki, Katsumi Yamashita, Kaori Fukuzawa, Kazutomo Takematsu, Hirofumi Watanabe, Naoki Taguchi, Yoshio Okiyama, Misako Tsuboi, Tatsuya Nakano, Shigenori Tanaka

Chemical Physics Letters　Vol. 493　No. 4-6　p. 346-352　2010/06　Research paper (scientific journal)

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

Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka

BIOPHYSICAL JOURNAL　Vol. 98　No. 3　p. 74A-74A　2010/01

Accuracy of fragmentation in ab initio calculations of hydrated sodium cation

Takatoshi Fujita, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

CHEMICAL PHYSICS LETTERS　Vol. 478　No. 4-6　p. 295-300　2009/08　Research paper (scientific journal)

Fragment Molecular Orbital (FMO) and FMO-MO Calculations of DNA: Accuracy Validation of Energy and Interfragment Interaction Energy

Toshio Watanabe, Yuichi Inadomi, Hiroaki Umeda, Kaori Fukuzawa, Shigenori Tanaka, Tatsuya Nakano, Umpei Nagashima

JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE　Vol. 6　No. 6　p. 1328-1337　2009/06　Research paper (scientific journal)

Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding

Kazutomo Takematsu, Kaori Fukuzawa, Katsumi Omagari, Setsuko Nakajima, Katsuhisa Nakajima, Yuji Mochizuki, Tatsuya Nakano, Hirofumi Watanabe, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 113　No. 15　p. 4991-4994　2009/04　Research paper (scientific journal)

Developments of FMO methodology and graphical user interface in ABINIT-MP

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　p. 37-62　2009　Part of collection (book)

Analysis of Mutation Mechanisms of Influenza Virus Based on the Fragment Molecular Orbital Method

Tanaka Shigenori, Mochizuki Yuji, Fukuzawa Kaori, Yamashita Katsumi, Nakano Tatsuya

Annual Report of the Earth Simulator Center April　Vol. 2010　2009

7 Application of the FMO Method to Specific Molecular Recognition of Biomacromolecules

Fukuzawa Kaori, Mochizuki Yuji, Nakano Tatsuya, Tanaka Shigenori

The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems　p. 133-169　2009　Part of collection (book)

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

Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori

Seibutsu Butsuri　Vol. 49　No. supplement　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

Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori

Seibutsu Butsuri　Vol. 49　No. supplement　2009

Discovery of boron-conjugated 4-anilinoquinazoline as a prolonged inhibitor of EGFR tyrosine kinase

Hyun Seung Ban, Taikou Usui, Wataru Nabeyama, Hidetoshi Morita, Kaori Fukuzawa, Hiroyuki Nakamura

ORGANIC & BIOMOLECULAR CHEMISTRY　Vol. 7　No. 21　p. 4415-4427　2009　Research paper (scientific journal)

Fragment Molecular Orbital Calculations on Red Fluorescent Proteins (DsRed and mFruits)

Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Kaori Fukuzawa, Takeshi Ishikawa, Minoru Sakurai, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 113　No. 4　p. 1153-1161　2009/01　Research paper (scientific journal)

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

Yoshio Okiyama, Hirofumi Watanabe, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Takeshi Ishikawa, Kuniyoshi Ebina, Shigenori Tanaka

Chemical Physics Letters　Vol. 467　No. 4-6　p. 417-423　2009/01　Research paper (scientific journal)

Ab initio fragment molecular orbital study of molecular interactions in liganded retinoid X receptor: Specification of residues associated with ligand inducible information transmission

Mika Ito, Kaori Fukuzawa, Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 112　No. 38　p. 12081-12094　2008/09　Research paper (scientific journal)

COMP 246-Simulation study of RNA-binding protein by fragment molecular orbital (FMO) method

Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY　Vol. 236　2008/08

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

COMPUTATIONAL BIOLOGY AND CHEMISTRY　Vol. 32　No. 3　p. 198-211　2008/06　Research paper (scientific journal)

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

COMPUTATIONAL BIOLOGY AND CHEMISTRY　Vol. 32　No. 3　p. 149-158　2008/06　Research paper (scientific journal)

Large scale FMO-MP2 calculations on a massively parallel-vector computer

Yuji Mochizuki, Katsumi Yamashita, Tadashi Murase, Tatsuya Nakano, Kaori Fukuzawa, Kazutomo Takematsu, Hirofumi Watanabe, Shigenori Tanaka

CHEMICAL PHYSICS LETTERS　Vol. 457　No. 4-6　p. 396-403　2008/05　Research paper (scientific journal)

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 A　Vol. 112　No. 10　p. 1986-1998　2008/03　Research paper (scientific journal)

Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery

Bernhard Fischer, Kaori Fukuzawa, Wolfgang Wenzel

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　Vol. 70　No. 4　p. 1264-1273　2008/03　Research paper (scientific journal)

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 CHEMISTRY　Vol. 130　No. 1-2　p. 1-9　2007/10　Research paper (scientific journal)

Intra- and intermolecular interactions between Cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study (vol 27, pg 948, 2006)

Kaori Fukuzawa, Yuto Komeiji, Yujj Mochizuki, Akifumi Kato, Tatsuya Nakano, Shigenori Tanaka

JOURNAL OF COMPUTATIONAL CHEMISTRY　Vol. 28　No. 13　p. 2237-2239　2007/10

DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations

Toshio Watanabe, Yuichi Inadomi, Kaori Fukuzawa, Tatsuya Nakano, Shigenori Tanaka, Lennart Nilsson, Umpei Nagashima

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 111　No. 32　p. 9621-9627　2007/08　Research paper (scientific journal)

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 B　Vol. 111　No. 13　p. 3525-3533　2007/04　Research paper (scientific journal)

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))

Fukuzawa, K., Komeiji, Y., Mochizuki, Y., Kato, A., Nakano, T., Tanaka, S.

Journal of Computational Chemistry　Vol. 28　No. 13　2007　Research paper (scientific journal)

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)

Kurisaki Ikuo, Fukuzawa Kaori, Nakano Tatsuya, Mochizuki Yuji, Watanabe Hirofumi, Tanaka Shigenori

Seibutsu Butsuri　Vol. 47　No. supplement　2007

Comparison of epitope structures of H3HAs through protein modeling of influenza a virus hemagglutinin: Mechanism for selection of antigenic variants in the presence of a monoclonal antibody

Setsuko Nakajima, Katsuhisa Nakajima, Eri Nobusawa, Jin Zhao, Shigenori Tanaka, Kaori Fukuzawa

MICROBIOLOGY AND IMMUNOLOGY　Vol. 51　No. 12　p. 1179-1187　2007　Research paper (scientific journal)

Application of the fragment molecular orbital method for determination of atomic charges on polypeptides

Yoshio Okiyama, Hirofumi Watanabe, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Takeshi Ishikawa, Shigenori Tanaka, Kuniyoshi Ebina

Chemical Physics Letters　Vol. 449　No. 4-6　p. 329-335　2007　Research paper (scientific journal)

Effects of Point Mutations on the Binding Energies of Estrogen Receptor with Estradiol

K. Maeda, A. Schug, H. Watanabe, K. Fukuzawa, Y. Mochizuki, T. Nakano, S. Tanaka

J. Comput. Chem. Jpn.　Vol. 6　No. 1　p. 33-46　2007　Research paper (scientific journal)

Applications of the Fragment Molecular Orbital Method for Bio-Macromolecules

FUKUZAWA Kaori, NAKANO Tatsuya, KATO Akifumi, MOCHIZUKI Yuji, TANAKA Shigenori

Journal of Chemical Software　Vol. 6　No. 3　p. 185-198　2007　Research paper (scientific journal)

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, Japan　Vol. 6　No. 3　p. 173-184　2007　Research paper (scientific journal)

フラグメント分子軌道法プログラムABINIT-MPによる受容体－リガンド相互作用解析

福澤薫, 中野達也

CBI学会ソリューションガイドモノグラフ「構造に基づく薬の設計法（SBDD）の進歩」＋ソリューションガイド　2007　Research paper (other academic)

Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method (vol 110, pg 24276, 2006)

Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka, Kazuo Kitaura, Tatsuya Nakano

JOURNAL OF PHYSICAL CHEMISTRY B　Vol. 110　No. 47　p. 24276-24276　2006/11

Advanced scientific computational methods and their applications to nuclear technologies - (6) Simulation methods in discretized systems, (2)

Seiichi Koshizuka, Kiyoshi Matsubara, Kaori Fukuzawa

JOURNAL OF THE ATOMIC ENERGY SOCIETY OF JAPAN　Vol. 48　No. 9　p. 684-689　2006/09　Research paper (scientific journal)

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 B　Vol. 110　No. 32　p. 16102-16110　2006/08　Research paper (scientific journal)

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 LETTERS　Vol. 427　No. 1-3　p. 159-165　2006/08　Research paper (scientific journal)

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 CHEMISTRY　Vol. 27　No. 8　p. 948-960　2006/06　Research paper (scientific journal)

Drug discovery using grid technology

Hitoshi Goto, Sigeaki Obata, Toshiyuki Kamakura, Naofumi Nakayama, Mitsuhisa Sato, Yoshihiro Nakajima, Umpei Nagashima, Toshio Watanabe, Yuichi Inadomi, Masakatsu Ito, Takeshi Nishikawa, Tatsuya Nakano, Lennart Nilsson, Shigenori Tanaka, Kaori Fukuzawa, Yuichiro Inagaki, Michiaki Hamada, Hiroshi Chuman

Modern Methods for Theoretical Physical Chemistry of Biopolymers　p. 227-248　2006　Part of collection (book)

Developments and applications of ABINIT-MP software based on the fragment molecular orbital method

Tatsuya Nakano, Yuji Mochizuki, Kaori Fukuzawa, Shinji Amari, Shigenori Tanaka

Modern Methods for Theoretical Physical Chemistry of Biopolymers　p. 39-52　2006　Part of collection (book)

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 MODELING　Vol. 46　No. 1　p. 221-230　2006/01　Research paper (scientific journal)

量子化学計算（FMO法）

中野達也, 望月祐志, 甘利真司, 福澤薫

東京大学情報基盤センター・スーパーコンピューティングニュース　2006　Research paper (bulletin of university, research institution)

分子軌道法

松原聖, 福澤薫

原子力学会誌　2006　Research paper (scientific journal)

BioStation Viewer: Analysis and Visualization for Interactions of Bio-Macromolecules

KATO Akifumi, FUKUZAWA Kaori, MOCHIZUKI Yuji, AMARI Shinji, NAKANO Tatsuya

Transactions of Visualization Society of Japan　Vol. 26　No. 101　p. 124-129_1　2006　Research paper (scientific journal)

1A configuration analysis for fragment interaction

Y Mochizuki, K Fukuzawa, A Kato, S Tanaka, K Kitaura, T Nakano

CHEMICAL PHYSICS LETTERS　Vol. 410　No. 4-6　p. 247-253　2005/07　Research paper (scientific journal)

Numerical methodology of sodium-water reaction with multiphase flow analysis

T Takata, A Yamaguchi, K Fukuzawa, K Matsubara

NUCLEAR SCIENCE AND ENGINEERING　Vol. 150　No. 2　p. 221-236　2005/06　Research paper (scientific journal)

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)　Vol. ES-P23,　2005　Research paper (international conference proceedings)

Ab initio quantum mechanical study of the binding energies of human estrogen receptor alpha with its ligands: An application of fragment molecular orbital method

K Fukuzawa, K Kitaura, M Uebayasi, K Nakata, T Kaminuma, T Nakano

JOURNAL OF COMPUTATIONAL CHEMISTRY　Vol. 26　No. 1　p. 1-10　2005/01　Research paper (scientific journal)

量子化学計算でみるエストロゲン受容体と化学物質の相互作用

福澤薫

バイオニクス　Vol. 2　No. 7　p. 65-67　2005　Research paper (scientific journal)

Ab initio potential energy surfaces of the ion-molecule reaction: C2H2+O+

K Fukuzawa, T Matsushita, K Morokuma

JOURNAL OF CHEMICAL PHYSICS　Vol. 121　No. 7　p. 3117-3129　2004/08　Research paper (scientific journal)

非経験的フラグメント分子軌道法によるエストロゲン受容体とリガンドとの結合性予測

長嶋雲兵, 福澤薫, 中野達也

ファインケミカル　Vol. 33　No. 4　p. 44-52　2004　Research paper (scientific journal)

Fragment molecular orbital study of the binding energy of ligands to the estrogen receptor

K Fukuzawa, K Kitaura, K Nakata, T Kaminuma, T Nakano

PURE AND APPLIED CHEMISTRY　Vol. 75　No. 11-12　p. 2405-2410　2003/11　Research paper (scientific journal)

Fragment molecular orbital method: application to molecular dynamics simulation, 'ab initio FMO-MD'

Y Komeiji, T Nakano, K Fukuzawa, Y Ueno, Y Inadomi, T Nemoto, M Uebaysai, DG Fedorov, K Kitaura

CHEMICAL PHYSICS LETTERS　Vol. 372　No. 3-4　p. 342-347　2003/04　Research paper (scientific journal)

DNA鎖の第一原理計算の現状と将来

田中成典, 福澤薫, 中野達也, 栗田典之

表面科学　2003　Research paper (scientific journal)

Fragment molecular orbital method: use of approximate electrostatic potential

T Nakano, T Kaminuma, T Sato, K Fukuzawa, Y Akiyama, M Uebayasi, K Kitaura

CHEMICAL PHYSICS LETTERS　Vol. 351　No. 5-6　p. 475-480　2002/01　Research paper (scientific journal)

An ab initio and experimental study of vibrational effects in low energy O++C2H2 charge-transfer collisions

K Fukuzawa, T Matsushita, K Morokuma, DJ Levandier, YH Chiu, RA Dressler, E Murad, A Midey, S Williams, AA Viggiano

JOURNAL OF CHEMICAL PHYSICS　Vol. 115　No. 7　p. 3184-3194　2001/08　Research paper (scientific journal)

Ion-molecule reactions producing HC3NH+ in interstellar space: Forbiddenness of the reaction between cyclic C3H3+ and the N atom

N Takagi, K Fukuzawa, Y Osamura, HF Schaefer

ASTROPHYSICAL JOURNAL　Vol. 525　No. 2　p. 791-798　1999/11　Research paper (scientific journal)

A molecular orbital study of the HC3NH+ + e(-) dissociative recombination and its role in the production of cyanoacetylene isomers in interstellar clouds

Y Osamura, K Fukuzawa, R Terzieva, E Herbst

ASTROPHYSICAL JOURNAL　Vol. 519　No. 2　p. 697-704　1999/07　Research paper (scientific journal)

Are neutral-neutral reactions effective for the carbon-chain growth of cyanopolyynes and polyacetylenes in interstellar space?

K Fukuzawa, Y Osamura, HF Schaefer

ASTROPHYSICAL JOURNAL　Vol. 505　No. 1　p. 278-285　1998/09　Research paper (scientific journal)

Molecular orbital study of neutral-neutral reactions concerning HC3N formation in interstellar space

K Fukuzawa, Y Osamura

ASTROPHYSICAL JOURNAL　Vol. 489　No. 1　p. 113-121　1997/11　Research paper (scientific journal)