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PAICSが使用されている論文等のリストです。これ以外に、PAICSが使用されている論文をご存じの方がいらっしゃいましたら、ご連絡頂けると幸いです（ishi.qchem [at] gmail.com） |
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英文論文（理論・アルゴリズム・プログラム開発） |
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| 1 |
Theoretical study of the prion protein based on the fragment molecular orbital method,
T. Ishikawa, T. Ishikura, K. Kuwata,
J. Comput. Chem., 30 (2009) 2594-2601
(DOI: 10.1002/jcc.21265) |
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| 2 |
Fragment molecular orbital calculation using the RI-MP2 method,
T. Ishikawa, K. Kuwata,
Chem. Phys. Lett., 474 (2009) 195-198
(DOI: 10.1016/j.cplett.2009.04.045) |
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| 3 |
Acceleration of monomer self-consistent charge process in fragment molecular orbital method,
T. Ishikawa, K. Kuwata,
C.B.I.J., 10 (2010) 24-31
(DOI: 10.1273/cbij.10.24) |
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| 4 |
Partial energy gradient based on the fragment molecular orbital method: application to geometry optimization,
T. Ishikawa, N. Yamamoto, K. Kuwata,
Chem. Phys. Lett., 500 (2010) 149-154
(DOI: 10.1016/j.cplett.2010.09.071) |
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| 5 |
RI-MP2 Gradient Calculation of Large Molecules using the Fragment Molecular Orbital Method,
T. Ishikawa, K. Kuwata,
J. Phys. Chem. Lett., 3 (2012) 375-379
(DOI: 10.1021/jz201697x) |
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| 6 |
A Minimal Implementation of the AMBER-PAICS Interface for Ab Initio FMO-QM/MM-MD Simulation,
T. Okamoto, T. Ishikawa, Y. Koyano, N. Yamamoto, K. Kuwata, M. Nagaoka,
Bull. Chem. Soc. Jap., 86 (2013) 210-222
(DOI: 10.1246/bcsj.20120216) |
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| 7 |
A Mini-review on Chemoinformatics Approaches for Drug Discovery,
N. Kawashita, H. Yamasaki, T. Miyao, K. Kawai, Y. Sakae, T. Ishikawa, K. Mori, S. Nakamura, H. Kaneko,
J. Comput. Aided Chem., 16 (2015) 15-29
(DOI: 10.2751/jcac.16.15) |
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| 8 |
Ab initio quantum chemical calculation of electron density, electrostatic potential, and electric field of biomolecule based on fragment molecular orbital method,
T. Ishikawa,
Int. J. Quantum Chem., 118 (2018) e25535
(DOI: 10.1002/qua.25535)
(selected as cover image)
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| 9 |
RI-MP3 calculations of biomolecules based on the fragment molecular orbital method,
T. Ishikawa, K. Sakakura, Y. Mochizuki,
J. Comput. Chem., 186 (2018) 613-632
(DOI: 10.1002/jcc.25368) |
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| 10 |
Development of analysis toolkit to visualize interaction energies generated by fragment molecular orbital calculations,
T. Tokiwa, S. Nakano, Y. Yamamoto, T. Ishikawa, S. Ito, V. Sladek, K. Fukuzawa, Y. Mochizuki, H. Tokiwa, F. Misaizu, Y. Shigeta,
J. Chem. Inf. Model. 59 (2019) 25-30
(DOI: 10.1021/acs.jcim.8b00649) |
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| 11 |
A novel method for analysis of the electrostatic complementarity of protein-protein interaction based on fragment molecular orbital method,
T. Ishikawa,
Chem. Phys. Lett., 761 (2020) 138103,
(DOI: 10.3389/fmicb.2020.01830) |
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| 12 |
Visualization of the interfacial electrostatic complementarity: A method for analysis of protein-protein interaction based on ab initio quantum chemical calculations,
H. Ozono, T. Ishikawa,
J. Chem. Theory Comput. 17 (2021) 5600-5610
(DOI: 10.1021/acs.jctc.1c00475) |
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| 13 |
Quantification and Neutralization of Interfacial Electrostatic Potential and Visualization of Dispersion Interaction in VIINEC,
H. Ozono, K. Mimoto, T. Ishikawa,
J. Chem. Phys. B, 126 (2022) 8415-8426
(DOI: 10.1021/acs.jpcb.2c05033) |
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英文論文（応用研究） |
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| 1 |
Interaction analysis of the native structure of prion protein with quantum chemical calculations,
T. Ishikawa, K. Kuwata,
J. Chem. Theor. Comput., 6 (2010) 538-547
(DOI: 10.1021/ct900456v) |
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| 2 |
Origin of the inhibitory activity of 4-O-substituted sialic derivatives of human parainfluenza virus
Y. Itoh, A. Sando, K. Ikeda, T. Suzuki, H. Tokiwa,
Glycoconj J., 29 (2012) 237
(DOI: 10.1007/s10719-012-9384-3) |
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| 3 |
Theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method,
T. Ishikawa, R. R. Burri, Yuji O. Kamatari, S. Sakuraba, N. Matubayasi, A. Kitao., K. Kuwata,
Phys. Chem. Chem. Phys., 15, (2013) 3646-3654
(DOI: 10.1039/C3CP42761G) |
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| 4 |
Catalytic preference of Salmonella typhimurium LT2 sialidase for N -acetylneuraminic acid residues over N -glycolylneuraminic acid residues,
A. Minami, S. Ishibashi, K. Ikeda, E. Ishitsubo, T. Hori, H. Tokiwa, R. Taguchi, D. Ieno, T. Otsubo, Y. Matsuda, S. Sai, M. Inada, T. Suzuki,
FEBS Open Bio., 3, (2013) 231-236
(DOI: 10.1016/j.fob.2013.05.002) |
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| 5 |
Computational design of a sulfoglucuronide derivative fitting into a hydrophobic pocket of dengue virus E protein,
T. Abe, A. Sando, F. Teraoka, T. Otsubo, K. Morita, H. Tokiwa, K. Ikeda, T. Suzuki, K. I.P.J. Hidari,
Biochem. Biophys. Res. Comm., 449,(2014) 32-37,
(DOI: 10.1016/j.bbrc.2014.04.122) |
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| 6 |
Novel Approach for Identifying Key Residues in Enzymatic Reactions: Proton Abstraction in Ketosteroid Isomerase,
M. Ito, T. Brinck,
J. Chem. Phys. B, 118, (2014) 13050-13058
(DOI: 10.1021/jp508423s) |
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| 7 |
Protein stabilization utilizing a redefined codon,
K. Ohtake, A. Yamaguchi, T. Mukai, H. Kashimura, N. Hirano, M. Haruki, S. Kohashi, K. Yamagishi, K. Murayama, Y. Tomabechi, T. Itagaki, R. Akasaka, M. Kawazoe, C. Takemoto, M. Shirouzu, S. Yokoyama, K. Sakamoto,
Scientific Reports, 5, (2015) 9762
(DOI: 10.1038/srep09762) |
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| 8 |
Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline D-peptidase from Bacillus cereus DF4-B,
S. Nakano, S. Okazaki, E. Ishitsubo, N. Kawahara, H. Komeda, H. Tokiwa, Y. Asano,
Scientific Reports, 5, (2015) 13836
(DOI: 10.1038/srep13836) |
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| 9 |
Molecular cloning and biochemical characterization of isoprene synthases from the tropical trees Ficus virgata, Ficus septica, and Casuarina equisetifolia,
H. Oku, M. Inafuku, T. Ishikawa, T. Takamine, M. Ishmael, M. Fukuta,
J. Plant Research, 128, (2015) 849
(DOI: 10.1007/s10265-015-0740-9) |
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| 10 |
Crystal structure of the N-myristoylated lipopeptide-bound MHC class I complex,
D. Morita, Y. Yamamoto, T. Mizutani, T. Ishikawa, J. Suzuki, T. Igarashi, N. Mori, T. Shiina, H. Inoko, H. Fujita, K. Iwai, Y. Tanaka, B. Mikami, M. Sugita,
Nat. Comm., 7 (2016) 10356
(DOI: 10.1038/ncomms10356) |
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| 11 |
Logical design of anti-prion agents using NAGARA,
B. Ma, K. Yamaguchi, M. Fukuoka, K. kuwata,
Biochem. Biophys. Res. Comm., 469 (2016) 930-935
(DOI: 10.1016/j.bbrc.2015.12.106) |
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| 12 |
Ca2+ monitoring in Plasmodium falciparum using the yellow cameleon-Nano biosensor,
K. Pandey, P. Ferreira, T. Ishikawa, T. Nagai, O. Kaneko, K. Yahata,
Sci. Rep., 6 (2016) 23454
(DOI: 10.1038/srep23454) |
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| 13 |
A Novel Potent and Highly Specific Inhibitor against Influenza Viral N1-N9 Neuraminidases: Insight into Neuraminidase-inhibitor Interactions,
N. Sriwilaijaroen, S. Magesh, A. Imamura, H. Ando, H. Ishida, M. Sakai, E. Ishitsubo, T. Hori, S. Moriya, T. Ishikawa, K. Kuwata, T. Odagiri, M. Tashiro, H. Hiramatsu, K. Tsukamoto, T. Miyagi, H. Tokiwa, M. Kiso, Y. Suzuki,
J. Med. Chem., 59 (2016) 4563-4577
(DOI: 10.1021/acs.jmedchem.5b01863) |
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| 14 |
Structure-based drug discovery for prion disease by using a novel binding simulation,
D. Ishibashi, T. Nakagaki, T. Ishikawa, R. Atarashi, K. Watanabe, F. Cruz, T. Hamada, N. Nishida,
EBioMedicine, 9 (2016) 238-249
(DOI: 10.1016/j.ebiom.2016.06.010) |
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| 15 |
Origin of Stereoselectivity and Substrate/ligand Recognition in an FAD-Dependent R-Selective Amine Oxidase,
S. Nakano, K. Yasukawa, T. Tokiwa, T. Ishikawa, E. Ishitsubo, N. Matsuo, S. Ito, H. Tokiwa, Y. Asano,
J. Phys. Chem. B, 120 (2016) 10736-10743
(DOI: 10.1021/acs.jpcb.6b09328) |
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| 16 |
Comparative Binding Analysis of Dipeptidyl Peptidase IV (DPP-4) with Antidiabetic Drugs −An Ab Initio Fragment Molecular Orbital Study,
S. Arulmozhiraja, N. Matsuo, E. Ishitsubo, S. Okazaki, H. Shimano, H. Tokiwa,
PLoS ONE, 11 (2016) e0166275
(DOI: 10.1371/journal.pone.0166275) |
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| 17 |
Identification of Small Molecule Inhibitors for Influenza A Virus Using In Silico and In Vitro Approaches,
J. N. Makau, K. Watanabe, T. Ishikawa, S. Mizuta, T. Hamada, N. Kobayashi, N. Nishida,
PLoS ONE, 12 (2017) e0173582
(DOI: 10.1371/journal.pone.0173582) |
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| 18 |
Computational study of the competitive binding of valproic acid glucuronide and carbapenem antibiotics to acylpeptide hydrolase,
T. Ishikawa, H. Otaki, S. Mizuta, M. Kuriyama, O. Onomura, N. Higfuchi, M. N. Nakashima, M. Nakashima, K. Ohyama,
Drug Metabolism and Pharmacokinetics, 32 (2017) 201-207
(DOI: 10.1016/j.dmpk.2017.04.002) |
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| 19 |
Product Release Mechanism Associated with Structural Changbes in Monomeric L-Threonine 3-Dehydrogenase,
T. Motoyama, S. Nakano, Y. Yamamoto, H. Tokiwa, Y. Asano, S. Ito,
Biochemistry, 56 (2017) 5758-5770
(DOI: 10.1021/acs.biochem.7b00832) |
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| 20 |
Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα,
Y. Yamamoto, K. Takei, S. Arulmozhiraja, V. Sladek, N. Matsuo, S.-i. Han, T. Matsuzaka, M. Sekiya, T. Tokiwa, M. Shoji, Y. Shigeta, Y. Nakagawa, H. Tokiwa, H. Shimano,
Biochem. Bioph. Res. Comm., 499 (2018) 239-245
(DOI: 10.1016/j.bbrc.2018.03.135) |
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| 21 |
Molecular characterization of cytosolic cysteine synthase in Mimosa pudica,
Md. Harun-Ur-Rashid, H. Iwasaki, S. Oogai, M. Fukuta, S. Parveen, Md. Amzad Hossain, T. Anai, H. Oku,
J. Plant Res., 131 (2018) 319-329
(DOI: 10.1007/s10265-017-0986-5) |
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| 22 |
Cytosolic Cysteine Synthase Switch Cysteine and Mimosine Production in Leucaena leucocephala,
Md. Harun-Ur-Rashid, H. Iwasaki, S. Parveen, S. Oogai, M. Fukuta, Md. Amzad Hossain, T. Anai, H. Oku,
Appl. Biochem. Biotech., 186 (2018) 613-632
(DOI: 10.1007/s12010-018-2745-z) |
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| 23 |
Fragment Molecular Orbital Study of the Interaction Between Sarco/Endoplasmic Reticulum Ca2+-ATPase and Its Inhibitor Thapsigargin Toward Anti-Malarial Development,
T. Ishikawa, S. Mizuta, O. Kaneko, K. Yahata,
J. Phys. Chem. B, 122 (2018) 7970-7977
(DOI: 10.1021/acs.jpcb.8b04509) |
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| 24 |
Prediction of ALK Mutations Mediating ALK-TKIs Resistance and Drug Re-Purposing to Overcome the Resistance,
K. Okuda, M. Araki, T. Sakashita, B. Ma, R. Kanada, N. Yanagitani, A. Horiike, S. Koike, T. Oh-hara, K. Watanabe, K. Tamai, M. Maemondo, M. Nishio, T. Ishikawa, Y. Okuno, N. Fujita, R. Katayama,
EBioMedicine, 41 (2019) 105-119
(DOI: 10.1016/j.ebiom.2019.01.019) |
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| 25 |
A medical chaperone for prion proteins decelerates the progress of transmissible spongiform encephalopathy,
K. Yamaguchi, Y. O. Kamatari, F. Ono, H. Shibata, T. Fuse, A. Elhelaly, M. Fukuoka, T. Kimura, J. Hosokawa-Muto, T. Ishikawa, M. Tobiume, Y. Takeuchi, Y. Matsuyama, D. Ishibashi, N. Nishida, K. Kuwata,
Nat. Biomed. Eng., 3 (2019) 206-219
(DOI: 10.1038/s41551-019-0349-8) |
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| 26 |
Synthesis and characterization of small interfering RNAs with haloalkyl groups at their 3-dangling ends,
A. Chandela, T. Watanabe, K. Yamagishi, Y. Ueno,
Bioorg. Med. Chem., 27 (2019) 1341-1349
(DOI: 10.1016/j.bmc.2019.02.037) |
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| 27 |
Roles of YIGL sequence of Ebola virus VP40 on genome replication and particle production,
S. Urata, T. Ishikawa, J. Yasuda*,
J. Gen. Virol., 100 (2019) 1099-1111
(DOI: 10.1099/jgv.0.001286) |
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| 28 |
Inhibition of Niemann-Pick C1-Like 1 by Ezetimibe Reduces Dietary 5β,6β-Epoxycholesterol Absorption in Rats,
Bungo Shirouchi, Yumiko Furukawa, Yuri Nakamura, Asuka Kawauchi, Katsumi Imaizumi, Hirosuke Oku, Masao Sato*,
Cardiovascular Drugs and Therapy, 33 (2019) 35-44
(DOI: 10.1007/s10557-019-06854-4) |
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| 29 |
Molecular characterization of mimosinase and cystathionine β-lyase in the Mimosoideae subfamily member Mimosa pudica,
Shigeki Oogai, Masakazu Fukuta, Keiichi Watanabe, Masashi Inafuku, Hirosuke Oku*,
J. Plant Res., 132 (2019) 667-680
(DOI: 10.1007/s10265-019-01128-4) |
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| 30 |
Binding interaction analysis of RNA aptamer-Fc region of human immunoglobulin G using fragment molecular orbital calculation,
H. Yoshida, K. Sato, T. Ishikawa, T. Sakamoto, K. Yamagishi*,
Chem. Phys. Lett., 738 (2020) 136854
(DOI: 10.1016/j.cplett.2019.136854) |
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| 31 |
Elucidation of Molecular Mechanism of a Selective PPARα Modulator, Pemafibrate, through Combinational Approaches of X-ray Crystallography, Thermodynamic Analysis, and First-Principle Calculations,
Mayu Kawasaki, Akira Kambe, Yuta Yamamoto, Sundaram Arulmozhiraja, Sohei Ito, Yoshimi Nakagawa, Hiroaki Tokiwa, Shogo Nakano*, Hitoshi Shimano*,
Int. J. Mol. Sci., 21 (2020) 361
(DOI: 10.3390/ijms21010361) |
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| 32 |
Novel compounds identified by structure-based prion disease drug discovery using in silico screening delay the progression of an illness in prion-infected mice,
D. Ishibashi*, T. Ishikawa, S. Mizuta, H. Tange, T. Nakagaki, T. Hamada, N. Nishida,
Neurotherapeutics, 17 (2020) 1836
(DOI: 10.1007/s13311-020-00903-9) |
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| 33 |
Measles Virus Hemagglutinin Protein Establishes a Specific Interaction With the Extreme N-Terminal Region of Human Signaling Lymphocytic Activation Molecule to Enhance Infection,
F. Seki, Y. Yamamoto, H. Fukuhara, K. Ohishi, T. Maruyama, K. Maenaka, H. Tokiwa, and M. Takeda,
Front. Microbiol., 11 (2020) 183014
(DOI: 10.3389/fmicb.2020.01830) |
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| 34 |
Computational Analysis Reveals a Critical Point Mutation in the N-Terminal Region of the Signaling Lymphocytic Activation Molecule Responsible for the Cross-Species Infection with Canine Distemper Virus,
Y. Yamamoto, S. Nakano, F. Seki, Y. Shigeta, S. Ito, H. Tokiwa, M. Takeda,
Molecules, 26 (2021) 1262
(DOI: 10.3390/molecules26051262) |
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| 35 |
The transcriptional corepressor CtBP2 serves as a metabolite sensor orchestrating hepatic glucose and lipid homeostasis,
Motohiro Sekiya, Kenta Kainoh, Takehito Sugasawa, Ryunosuke Yoshino, Takatsugu Hirokawa, Hiroaki Tokiwa, Shogo Nakano, Satoru Nagatoishi, Kouhei Tsumoto, Yoshinori Takeuchi, Takafumi Miyamoto, Takashi Matsuzaka, Hitoshi Shimano,
Nat. Comm. 12 (2021) 6315
(DOI: 10.1038/s41467-021-26638-5) |
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| 36 |
Application of Visualization of the Interfacial Electrostatic Complementarity to Molecular Interaction Analysis on SARS-CoV-2 Spike Protein Receptor Binding Domain,
T. Ishikawa, H. Ozono, K. Akisawa, R. Hatada, K. Okuwaki, Y. Mochizuki,
J. Phys. Chem. Lett., 12 (2021) 11267
(DOI: 10.1021/acs.jpclett.1c02788) |
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| 37 |
Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations,
Biao Ma, Kei Terayama*, Shigeyuki Matsumoto, Yuta Isaka, Yoko Sasakura, Hiroaki Iwata, Mitsugu Araki, and Yasushi Okuno*,
J. Chem. Inf. Model., 61 (2021) 3304
(DOI: 10.1021/acs.jpclett.1c02788) |
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| 38 |
Isolation and characterization of mimosine degrading enzyme from Arthrobacter sp. Ryudai-S1,
S. Oogai, M. Fukuta, M. Inafuku, H. Oku
World J. Microbiol. Biotechnol., 38 (2022) 172
(DOI: 10.1007/s11274-022-03344-y) |
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| 39 |
Insights into the molecular interaction of cyclodextran with a guest molecule: A computational study,
W. Imamura, T. Yamasaki, H. Kato, T. Ishikawa*,
Carbohydrate Polymers, 301A (2023) 120315,
(DOI: 10.1016/j.carbpol.2022.120315) |
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| 40 |
Molecular characteristics of isoprene synthase and its control effects on isoprene emissions from tropical trees, ,
Hirosuke Oku, Ishmael Mutanda, Masashi Inafuku ,
Journal of Plant Research, 136 (2023) 63,
(DOI: 10.1007/s10265-022-01418-4) |
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| 41 |
Computational study on the inhibition mechanism of cyclodextran against GTF-SI from Streptococcus mutans focusing on the glucan-binding domain, ,
W. Imamura, T. Yamasaki, H. Kato, T. Ishikawa*,
Carbohydrate Polymer Technologies and Applications, in press,
(DOI: 10.1016/j.carpta.2024.100473) |
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その他の和文論文（総説・解説など） |
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| 1 |
フラグメント分子軌道法プログラム「PAICS」と統合創薬プログラム「NAGARA」,
石川岳志, 石倉孝和, 桑田一夫, MOLECULAR SCIENCE 5, NP0015 (2011),
(PDF) |
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| 2 |
量子創薬−論理的形態制御学の原理−,
桑田一夫, YAKUGAKU ZASSI, 132 (2012) 873-879,
(DOI: 10.1248/yakushi.132.873) |
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| 3 |
フラグメント分子軌道法に基づく QM/MM 分子動力学計算： AMBER-PAICS インターフェースの構築,
石川岳志, MOLECULAR SCIENCE 5, CICSJ Bulletin, 31（2013）73-77,
(J-STAGE) |
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| 4 |
FMO法を用いた核内受容体−リガンド間の相互作用解析,
吉田 尚恵, 春木 満, 山岸 賢司, J. Comput. Chem. Jpn., 13（2014）305,
(DOI: 10.2477/jccj.2014-0055) |
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| 5 |
ハロゲン原子導入によるタンパク質の構造安定化メカニズムの解明,
鷹觜順平, 小橋創介, 石川岳志, 坂本健作, 山岸賢司, J. Comput. Chem. Jpn., 13（2014）308-309,
(DOI: 10.2477/jccj.2014-0056) |
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| 6 |
フラグメント分子軌道法の新規薬剤開発への応用,
石川岳志, YAKUGAKU ZASSI, 136 (2016) 121-130,
(DOI: 10.1248/yakushi.15-00230-5) |
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| 7 |
ソフトウエア紹介「生体分子量子化学計算プログラム「PAICS」の紹介」,
石川岳志, アンサンブル, 22 (2020) 345,
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