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Items: 1 to 20 of 98

1.

ATP Converts Aβ42 Oligomer into Off-Pathway Species by Making Contact with Its Backbone Atoms Using Hydrophobic Adenosine.

Kurisaki I, Tanaka S.

J Phys Chem B. 2019 Nov 21;123(46):9922-9933. doi: 10.1021/acs.jpcb.9b07984. Epub 2019 Nov 7.

PMID:
31642322
2.

Guidelines for creating artificial neural network empirical interatomic potential from first-principles molecular dynamics data under specific conditions and its application to α-Ag2Se.

Shimamura K, Fukushima S, Koura A, Shimojo F, Misawa M, Kalia RK, Nakano A, Vashishta P, Matsubara T, Tanaka S.

J Chem Phys. 2019 Sep 28;151(12):124303. doi: 10.1063/1.5116420.

PMID:
31575208
3.

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

Okiyama Y, Watanabe C, Fukuzawa K, Mochizuki Y, Nakano T, Tanaka S.

J Phys Chem B. 2019 Feb 7;123(5):957-973. doi: 10.1021/acs.jpcb.8b09326. Epub 2018 Dec 28.

PMID:
30532968
4.

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

Sheng Y, Watanabe H, Maruyama K, Watanabe C, Okiyama Y, Honma T, Fukuzawa K, Tanaka S.

Comput Struct Biotechnol J. 2018 Oct 13;16:421-434. doi: 10.1016/j.csbj.2018.10.003. eCollection 2018.

5.

Ab initio molecular dynamics study of prebiotic production processes of organic compounds at meteorite impacts on ocean.

Shimamura K, Shimojo F, Nakano A, Tanaka S.

J Comput Chem. 2019 Jan 15;40(2):349-359. doi: 10.1002/jcc.25606. Epub 2018 Oct 11.

PMID:
30306615
6.

Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors.

Xu F, Tanaka S, Watanabe H, Shimane Y, Iwasawa M, Ohishi K, Maruyama T.

Viruses. 2018 May 3;10(5). pii: E236. doi: 10.3390/v10050236.

7.

Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations.

Trajkovski M, Endoh T, Tateishi-Karimata H, Ohyama T, Tanaka S, Plavec J, Sugimoto N.

Nucleic Acids Res. 2018 May 4;46(8):4301-4315. doi: 10.1093/nar/gky250.

8.

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

Okiyama Y, Nakano T, Watanabe C, Fukuzawa K, Mochizuki Y, Tanaka S.

J Phys Chem B. 2018 Apr 26;122(16):4457-4471. doi: 10.1021/acs.jpcb.8b01172. Epub 2018 Apr 16.

PMID:
29558137
9.

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

Watanabe C, Watanabe H, Fukuzawa K, Parker LJ, Okiyama Y, Yuki H, Yokoyama S, Nakano H, Tanaka S, Honma T.

J Chem Inf Model. 2017 Dec 26;57(12):2996-3010. doi: 10.1021/acs.jcim.7b00110. Epub 2017 Dec 1.

PMID:
29111719
10.

Structural transition of solvated H-Ras/GTP revealed by molecular dynamics simulation and local network entropy.

Matsunaga S, Hano Y, Saito Y, Fujimoto KJ, Kumasaka T, Matsumoto S, Kataoka T, Shima F, Tanaka S.

J Mol Graph Model. 2017 Oct;77:51-63. doi: 10.1016/j.jmgm.2017.07.028. Epub 2017 Jul 29.

PMID:
28837923
11.
12.

Newly characterized interaction stabilizes DNA structure: oligoethylene glycols stabilize G-quadruplexes CH-π interactions.

Tateishi-Karimata H, Ohyama T, Muraoka T, Podbevsek P, Wawro AM, Tanaka S, Nakano SI, Kinbara K, Plavec J, Sugimoto N.

Nucleic Acids Res. 2017 Jul 7;45(12):7021-7030. doi: 10.1093/nar/gkx299.

13.

Meteorite impacts on ancient oceans opened up multiple NH3 production pathways.

Shimamura K, Shimojo F, Nakano A, Tanaka S.

Phys Chem Chem Phys. 2017 May 10;19(18):11655-11667. doi: 10.1039/c7cp00870h.

PMID:
28435960
14.

Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations.

Uehara S, Tanaka S.

J Chem Inf Model. 2017 Apr 24;57(4):742-756. doi: 10.1021/acs.jcim.6b00791. Epub 2017 Apr 7.

PMID:
28388074
15.

Meteorite Impact-Induced Rapid NH3 Production on Early Earth: Ab Initio Molecular Dynamics Simulation.

Shimamura K, Shimojo F, Nakano A, Tanaka S.

Sci Rep. 2016 Dec 14;6:38953. doi: 10.1038/srep38953.

17.

Reduced minimum model for the photosynthetic induction processes in photosystem I.

Matsuoka T, Tanaka S, Ebina K.

J Photochem Photobiol B. 2016 Jul;160:364-75. doi: 10.1016/j.jphotobiol.2016.04.009. Epub 2016 Apr 16.

PMID:
27183491
18.

Diffusion Monte Carlo study on temporal evolution of entropy and free energy in nonequilibrium processes.

Tanaka S.

J Chem Phys. 2016 Mar 7;144(9):094103. doi: 10.1063/1.4942861.

PMID:
26957153
19.

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.

Nakano M, Tateishi-Karimata H, Tanaka S, Tama F, Miyashita O, Nakano S, Sugimoto N.

Nucleic Acids Res. 2015 Dec 2;43(21):10114-25. doi: 10.1093/nar/gkv1133. Epub 2015 Nov 3.

20.

Effects of Bridge Functions on Radial Distribution Functions of Liquid Water.

Tanaka S, Nakano M.

Interdiscip Sci. 2015 Jun;7(2):152-6. doi: 10.1007/s12539-015-0013-2. Epub 2015 Jul 19.

PMID:
26188390

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