Molecular dynamics analysis to evaluate docking pose prediction.

Sakano T, Mahamood MI, Yamashita T, Fujitani H. Molecular dynamics analysis to evaluate docking pose prediction. Biophys Physicobiol. 2016 Jul 14;13:181-194. eCollection 2016.

Epiregulin Recognition Mechanisms by Anti-epiregulin Antibody 9E5: STRUCTURAL, FUNCTIONAL, AND MOLECULAR DYNAMICS SIMULATION ANALYSES.

Kado Y, Mizohata E, Nagatoishi S, Iijima M, Shinoda K, Miyafusa T, Nakayama T, Yoshizumi T, Sugiyama A, Kawamura T, Lee YH, Matsumura H, Doi H, Fujitani H, Kodama T, Shibasaki Y, Tsumoto K, Inoue T. Epiregulin Recognition Mechanisms by Anti-epiregulin Antibody 9E5: STRUCTURAL, FUNCTIONAL, AND MOLECULAR DYNAMICS SIMULATION ANALYSES. J Biol Chem. 2016 Jan 29;291(5):2319-30. doi: 10.1074/jbc.M115.656009. Epub 2015 Dec 1.

The feasibility of an efficient drug design method with high-performance computers.

Yamashita T, Ueda A, Mitsui T, Tomonaga A, Matsumoto S, Kodama T, Fujitani H. The feasibility of an efficient drug design method with high-performance computers. Chem Pharm Bull (Tokyo). 2015;63(3):147-55. doi: 10.1248/cpb.c14-00596.

Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses.

Nakayama T, Mizohata E, Yamashita T, Nagatoishi S, Nakakido M, Iwanari H, Mochizuki Y, Kado Y, Yokota Y, Satoh R, Tsumoto K, Fujitani H, Kodama T, Hamakubo T, Inoue T. Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses. Protein Sci. 2015 Mar;24(3):328-40. doi: 10.1002/pro.2619. Epub 2015 Jan 13.

Molecular dynamics simulation-based evaluation of the binding free energies of computationally designed drug candidates: importance of the dynamical effects.

Yamashita T, Ueda A, Mitsui T, Tomonaga A, Matsumoto S, Kodama T, Fujitani H. Molecular dynamics simulation-based evaluation of the binding free energies of computationally designed drug candidates: importance of the dynamical effects. Chem Pharm Bull (Tokyo). 2014;62(7):661-7.

On accurate calculation of the potential of mean force between antigen and antibody: A case of the HyHEL-10-hen egg white lysozyme system

T. Yamashita and H. Fujitani On accurate calculation of the potential of mean force between antigen and antibody: A case of the HyHEL-10-hen egg white lysozyme system Chem Phys Lett 2014, v. 609, pp. 50-53 https://doi.org/10.1016/j.cplett.2014.06.028

High Performance Computing for Drug Development on K computer

H. Fujitani, K. Shinoda, T. Yamashita, T. Kodama High Performance Computing for Drug Development on K computer J Phys: Conf Ser. 2013, 454, p. 012018
https://doi.org/10.1088/1742-6596/454/1/012018

Theoretical Study on the Photocyclization Mechanism of Diarylethenes with Transition Metal Substituents

M. Hatakeyama, S. Yokojima, K. Shinoda, T. Koike, M. Akita, S. Nakamura Theoretical Study on the Photocyclization Mechanism of Diarylethenes with Transition Metal Substituents

pi-Conjugation of two nitronyl nitroxides-attached diarylethenes.

Yokojima S, Kobayashi T, Shinoda K, Matsuda K, Higashiguchi K, Nakamura S. pi-Conjugation of two nitronyl nitroxides-attached diarylethenes. J Phys Chem B. 2011 May 12;115(18):5685-92. doi: 10.1021/jp2002707. Epub 2011 Mar 28.

Two distinct amyloid beta-protein (Abeta) assembly pathways leading to oligomers and fibrils identified by combined fluorescence correlation spectroscopy, morphology, and toxicity analyses.

Matsumura S, Shinoda K, Yamada M, Yokojima S, Inoue M, Ohnishi T, Shimada T, Kikuchi K, Masui D, Hashimoto S, Sato M, Ito A, Akioka M, Takagi S, Nakamura Y, Nemoto K, Hasegawa Y, Takamoto H, Inoue H, Nakamura S, Nabeshima Y, Teplow DB, et al. Two distinct amyloid beta-protein (Abeta) assembly pathways leading to oligomers and fibrils identified by combined fluorescence correlation spectroscopy, morphology, and toxicity analyses. J Biol Chem. 2011 Apr 1;286(13):11555-62. doi: 10.1074/jbc.M110.181313. Epub 2011 Feb 3.

Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors.

Ohno K, Mitsui T, Tanida Y, Matsuura A, Fujitani H, Niimi T, Orita M. Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors. J Mol Model. 2011 Feb;17(2):383-9. doi: 10.1007/s00894-010-0728-2. Epub 2010 May 18.

Massively parallel computation of absolute binding free energy with well-equilibrated states.

Fujitani H, Tanida Y, Matsuura A. Massively parallel computation of absolute binding free energy with well-equilibrated states. Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Feb;79(2 Pt 1):021914. Epub 2009 Feb 26.

High-Level ab Initio Calculations To Improve Protein Backbone Dihedral Parameters.

Fujitani H, Matsuura A, Sakai S, Sato H, Tanida Y. High-Level ab Initio Calculations To Improve Protein Backbone Dihedral Parameters. J Chem Theory Comput. 2009 Apr 14;5(4):1155-65. doi: 10.1021/ct8005437.

Theoretical investigation on photochromic diarylethene: A short review

S. Nakamura, S. Yokojima, K. Uchida, T. Tsujioka, A. Goldberg, A. Murakami, K. Shinoda, M. Mikami, T. Kobayashi, S Kobatake, K. Matsuda, and M. Irie Theoretical investigation on photochromic diarylethene: A short review

Direct calculation of the binding free energies of FKBP ligands.

Fujitani H, Tanida Y, Ito M, Jayachandran G, Snow CD, Shirts MR, Sorin EJ, Pande VS. Direct calculation of the binding free energies of FKBP ligands. J Chem Phys. 2005 Aug 22;123(8):084108.

A generalized Ornstein-Zernike integral equation study of atomic impurities in quantum fluids

K. Shinoda, S. Miura, and S. Okazaki A generalized Ornstein-Zernike integral equation study of atomic impurities in quantum fluids

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