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PAICS

Parallelized ab initio Calculation System based on FMO


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< 関連論文 >
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)
英文論文
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 with 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)
総説・解説・その他の和文論文など
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)
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)
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)
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)
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)
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)