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1 Theoretical study of the prion protein based on the fragment molecular orbital method, T. Ishikawa, T. Ishikura, and K. Kuwata, J. Comput. Chem., 30 (2009) 2594-2601 (DOI: 10.1002/jcc.21265)
2 Fragment molecular orbital calculation using the RI-MP2 method, T. Ishikawa and K. Kuwata, Chem. Phys. Lett., 474 (2009) 195-198 (DOI: 10.1016/j.cplett.2009.04.045)
3 Interaction analysis of the native structure of prion protein with quantum chemical calculations, T. Ishikawa and K. Kuwata, J. Chem. Theor. Comput., 6 (2010) 538-547 (DOI: 10.1021/ct900456v)
4 Acceleration of monomer self-consistent charge process in fragment molecular orbital method, T. Ishikawa and K. Kuwata, C.B.I.J., 10 (2010) 24-31 (DOI: 10.1273/cbij.10.24)
5 Partial energy gradient based on the fragment molecular orbital method: application to geometry optimization, T. Ishikawa, N. Yamamoto, and K. Kuwata, Chem. Phys. Lett., 500 (2010) 149-154 (DOI: 10.1016/j.cplett.2010.09.071)
6 RI-MP2 Gradient Calculation of Large Molecules using the Fragment Molecular Orbital Method, T. Ishikawa and K. Kuwata, J. Phys. Chem. Lett., 3 (2012) 375-379 (DOI: 10.1021/jz201697x)
7 Origin of the inhibitory activity of 4-O-substituted sialic derivatives of human parainfluenza virus Y. Itoh, A. Sando, K. Ikeda, T. Suzuki, and H. Tokiwa, Glycoconj J., 29 (2012) 237 (DOI: 10.1007/s10719-012-9384-3)
8 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, and M. Nagaoka, Bull. Chem. Soc. Jap., 86 (2013) 210-222 (DOI: 10.1246/bcsj.20120216)
9 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)
10 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)
11 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)
12 Novel Approach for Identifying Key Residues in Enzymatic Reactions: Proton Abstraction in Ketosteroid Isomerase, M. Ito and T. Brinck, J. Chem. Phys. B, 118, (2014) 13050-13058, (DOI: 10.1021/jp508423s)
13 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)
14 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)
15 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)
16 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)
17 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)
18 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)
19 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)
20 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, and Y. Suzuki, J. Med. Chem., 59 (2016) 4563-4577 (DOI: 10.1021/acs.jmedchem.5b01863)
21 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)
22 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)
23 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)
24 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)
25 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 and K. Ohyama, Drug Metabolism and Pharmacokinetics, 32 (2017) 201-207 (DOI: 10.1016/j.dmpk.2017.04.002)
26 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)
27 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)



28 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)
29 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)
30 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., online published (DOI: 10.1007/s12010-018-2745-z)
31 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)
32 RI-MP3 calculations of biomolecules based on the fragment molecular orbital method, T. Ishikawa, K. Sakakura, Y. Mochizuki, J. Comput. Chem., online published (DOI: 10.1002/jcc.25368)