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Items: 1 to 20 of 68

1.

Prediction of Passive Membrane Permeability by Semi-Empirical Method Considering Viscous and Inertial Resistances and Different Rates of Conformational Change and Diffusion.

Fukunishi Y, Mashimo T, Kurosawa T, Wakabayashi Y, Nakamura HK, Takeuchi K.

Mol Inform. 2020 Jan;39(1-2):e1900071. doi: 10.1002/minf.201900071. Epub 2019 Oct 14.

PMID:
31609549
2.

Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism.

Higo J, Kasahara K, Wada M, Dasgupta B, Kamiya N, Hayami T, Fukuda I, Fukunishi Y, Nakamura H.

Protein Eng Des Sel. 2019 Oct 11. pii: gzz029. doi: 10.1093/protein/gzz029. [Epub ahead of print]

PMID:
31608410
3.

Chemical modification-mediated optimisation of bronchodilatory activity of mepenzolate, a muscarinic receptor antagonist with anti-inflammatory activity.

Yamashita Y, Tanaka KI, Yamakawa N, Asano T, Kanda Y, Takafuji A, Kawahara M, Takenaga M, Fukunishi Y, Mizushima T.

Bioorg Med Chem. 2019 Aug 1;27(15):3339-3346. doi: 10.1016/j.bmc.2019.06.016. Epub 2019 Jun 8.

PMID:
31204225
4.
5.

Identification of Mepenzolate Derivatives With Long-Acting Bronchodilatory Activity.

Tanaka KI, Yamakawa N, Yamashita Y, Asano T, Kanda Y, Takafuji A, Kawahara M, Takenaga M, Fukunishi Y, Mizushima T.

Front Pharmacol. 2018 Apr 10;9:344. doi: 10.3389/fphar.2018.00344. eCollection 2018.

6.

Prediction of Protein-compound Binding Energies from Known Activity Data: Docking-score-based Method and its Applications.

Fukunishi Y, Yamashita Y, Mashimo T, Nakamura H.

Mol Inform. 2018 Jul;37(6-7):e1700120. doi: 10.1002/minf.201700120. Epub 2018 Feb 14.

7.

Quantitative Structure-activity Relationship (QSAR) Models for Docking Score Correction.

Fukunishi Y, Yamasaki S, Yasumatsu I, Takeuchi K, Kurosawa T, Nakamura H.

Mol Inform. 2017 Jan;36(1-2). doi: 10.1002/minf.201600013. Epub 2016 Apr 29.

8.

Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling.

Iida S, Mashimo T, Kurosawa T, Hojo H, Muta H, Goto Y, Fukunishi Y, Nakamura H, Higo J.

J Comput Chem. 2016 Dec 5;37(31):2687-2700. doi: 10.1002/jcc.24494. Epub 2016 Oct 13.

9.

Miscellaneous Topics in Computer-Aided Drug Design: Synthetic Accessibility and GPU Computing, and Other Topics.

Fukunishi Y, Mashimo T, Misoo K, Wakabayashi Y, Miyaki T, Ohta S, Nakamura M, Ikeda K.

Curr Pharm Des. 2016;22(23):3555-68. Review.

10.

Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method.

Nguyen H, Tran T, Fukunishi Y, Higo J, Nakamura H, Le L.

J Chem Inf Model. 2015 Sep 28;55(9):1936-43. doi: 10.1021/acs.jcim.5b00319. Epub 2015 Sep 8.

PMID:
26247106
11.

Structure-Based Development of a Protein-Protein Interaction Inhibitor Targeting Tumor Necrosis Factor Receptor-Associated Factor 6.

Moriya J, Takeuchi K, Tai K, Arai K, Kobayashi N, Yoneda N, Fukunishi Y, Inoue A, Kihara M, Murakami T, Chiba K, Shimada I.

J Med Chem. 2015 Jul 23;58(14):5674-83. doi: 10.1021/acs.jmedchem.5b00778. Epub 2015 Jul 14.

PMID:
26132273
12.

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking.

Higo J, Dasgupta B, Mashimo T, Kasahara K, Fukunishi Y, Nakamura H.

J Comput Chem. 2015 Jul 30;36(20):1489-501. doi: 10.1002/jcc.23948. Epub 2015 Jun 4.

PMID:
26045390
13.

Bongkrekic acid as a selective activator of the peroxisome proliferator-activated receptor ╬│ (PPAR╬│) isoform.

Okazaki H, Takeda S, Ikeda E, Fukunishi Y, Ishii H, Taniguchi A, Tokuyasu M, Himeno T, Kakizoe K, Matsumoto K, Shindo M, Aramaki H.

J Toxicol Sci. 2015 Apr;40(2):223-33. doi: 10.2131/jts.40.223.

14.

Prediction of synthetic accessibility based on commercially available compound databases.

Fukunishi Y, Kurosawa T, Mikami Y, Nakamura H.

J Chem Inf Model. 2014 Dec 22;54(12):3259-67. doi: 10.1021/ci500568d. Epub 2014 Dec 3.

PMID:
25420000
15.

Synthesis and biological comparison of enantiomers of mepenzolate bromide, a muscarinic receptor antagonist with bronchodilatory and anti-inflammatory activities.

Yamashita Y, Tanaka K, Asano T, Yamakawa N, Kobayashi D, Ishihara T, Hanaya K, Shoji M, Sugai T, Wada M, Mashimo T, Fukunishi Y, Mizushima T.

Bioorg Med Chem. 2014 Jul 1;22(13):3488-97. doi: 10.1016/j.bmc.2014.04.029. Epub 2014 Apr 30.

PMID:
24844758
16.

Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions.

Mashimo T, Fukunishi Y, Kamiya N, Takano Y, Fukuda I, Nakamura H.

J Chem Theory Comput. 2013 Dec 10;9(12):5599-609. doi: 10.1021/ct400342e. Epub 2013 Nov 19.

PMID:
26592294
17.

Structural insights into the function of a thermostable copper-containing nitrite reductase.

Fukuda Y, Tse KM, Lintuluoto M, Fukunishi Y, Mizohata E, Matsumura H, Takami H, Nojiri M, Inoue T.

J Biochem. 2014 Feb;155(2):123-35. doi: 10.1093/jb/mvt107. Epub 2013 Nov 30.

PMID:
24293549
18.

Improved estimation of protein-ligand binding free energy by using the ligand-entropy and mobility of water molecules.

Fukunishi Y, Nakamura H.

Pharmaceuticals (Basel). 2013 Apr 26;6(5):604-22. doi: 10.3390/ph6050604.

19.

Molecular modeling of vasopressin receptor and in silico screening of V1b receptor antagonists.

Hagiwara Y, Ohno K, Kamohara M, Takasaki J, Watanabe T, Fukunishi Y, Nakamura H, Orita M.

Expert Opin Drug Discov. 2013 Aug;8(8):951-64. doi: 10.1517/17460441.2013.799134. Epub 2013 May 17. Review.

PMID:
23682717
20.

LigandBox: A database for 3D structures of chemical compounds.

Kawabata T, Sugihara Y, Fukunishi Y, Nakamura H.

Biophysics (Nagoya-shi). 2013 Aug 7;9:113-21. doi: 10.2142/biophysics.9.113. eCollection 2013.

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