Basic Concept of the 4th Section

Mainly, we are conducting research on adverse effects of medicines using computer such as fragment molecular orbital method and maintain the NIHS network.

Major Research Projects

1.      Research on adverse effects of medicines using the fragment molecular orbital method

2.      Development of The Japanese Pharmacopoeia Seventeenth Edition (JP17) Name and Structure Database (JPDB) and Japanese Accepted Names for Pharmaceuticals (JAN) database (JANDB)

3.      Administrating and maintain the NIHS network (NIHS-NET)


STAFF
Section Chief
F Tatsuya NAKANO, Ph.D.

Research OfficerF Katsunori SEGAWA, Ph.D.

Research AssistantFYoshio Okiyama, Ph. D.

1. Research on adverse effects of medicines using the fragment molecular orbital method

 

2.     Development of The Japanese Pharmacopoeia Seventeenth Edition (JP17) Name and Structure Database (JPDB) and Japanese Accepted Names for Pharmaceuticals (JAN) database (JANDB)

              

Homepage of JP DB                                                   Homepage of JAN DB

3.     Administrating and maintain the NIHS network (NIHS-NET)

1j Nakata, K., Nakano, T. and Kaminuma, T.: Bull. Natl. Inst. Health Sci., 114, 53-61i1996j

2j Nakata, K., Nakano, T., Takai, T. and Kaminuma, T.: Bull. Natl. Inst. Health Sci., 116, 92-100i1998j

3j Nakata, K., Nakano, T., Takai, T., Komine, K. and Kaminuma, T.: Bull. Natl. Inst. Health Sci., 118, 107-116 i2000j

4j Segawa, K., Nakano, T., Hayashi, Y. and Nakata, K.: Bull. Natl. Inst. Health Sci., 122, 34-36i2004j

5)  Segawa, K., Nakano, T., Saito, Y.: Bull. Natl. Inst. Health Sci., 130, 75-77i2012j

Publications

[2010]

K. Yamagishi, K. Yamamoto, Y. Mochizuki, T. Nakano, S. Yamada, H. Tokiwa, "Flexible ligand recognition of peroxisome proliferator-activated receptor-g (PPARg)", Bioorg. Med. Chem. Lett. 20, 3344 (2010).

Y. Okiyama, T. Nakano, K. Yamashita, Y. Mochizuki, N. Taguchi, S. Tanaka, "Acceleration of fragment molecular orbital calculations with Cholesky decomposition approach", Chem. Phys. Lett. 490, 84-89 (2010).

Y. Mochizuki, K. Yamashita, K. Fukuzawa, K. Takematsu, H. Watanabe, N. Taguchi, Y. Okiyama, M. Tsuboi, T. Nakano, S. Tanaka, "Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA)", Chem. Phys. Lett. 493, 346-352 (2010)

H. Watanabe, Y. Okiyama, T. Nakano, S. Tanaka, gIncorporation of solvation effects into the fragment molecular orbital calculations with the PoissonBoltzmann equationh, Chem. Phys. Lett. 500, 116-119 (2010).

I. Kurisaki, K. Fukuzawa, T. Nakano, Y. Mochizuki, H. Watanabe, S. Tanaka, gFragment molecular orbital (FMO) study on stabilization mechanism of neuro-oncological ventral antigen (NOVA)RNA complex systemh, J. Mol. Struct. (THEOCHEM) 962, 45-55 (2010).

M. Sato, H. Yamataka, Y. Komeiji, Y. Mochizuki, T. Nakano, gDoes Amination of Formaldehyde Proceed Through a Zwitterionic Intermediate in Water? Fragment Molecular Orbital Molecular Dynamics Simulations by Using Constraint Dynamicsh, Chemistry A European Journal, 16, 6430-6433 (2010).

T. Ogawa, T. Nakano, gThe Extended Universal Force Field (XUFF): Theory and Applicationsh, Chem-Bio. Info. J. 10, 111-133 (2010).

[2009]

Y. Komeiji, T. Ishikawa, Y. Mochizuki, H. Yamataka, T. Nakano, gFragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvationh, J. Comput. Chem. 30, 40-50 (2009).

Y. Komeiji, Y. Mochizuki, T. Nakano, and D. G. Fedorov, gFragment Molecular Orbital-based Molecular Dynamics (FMO-MD), a quantum simulation tool for large molecular systemsh, J. Mol. Struct. (Theochem), 898, 2-7 (2009).

T. Fujita, K. Fukuzawa, Y. Mochizuki, T. Nakano, S. Tanaka, "Accuracy of fragmentation in ab initio calculations of hydrated sodium cation", Chem. Phys. Lett. 478 295-300 (2009).

T. Watanabe, Y. Inadomi, H. Umeda, K. Fukuzawa, S. Tanaka, T. Nakano, U. Nagashima, "Fragment Molecular Orbital (FMO) and FMO-MO Calculations of DNA: Accuracy Validation of Energy and Interfragment Interaction Energy", J. Comp. Theor. Nanosci. 6, 1328-1337 (2009).

K. Takematsu, K. Fukuzawa, K. Omagari, S. Nakajima, K. Nakajima, Y. Mochizuki, T. Nakano, H. Watanabe, S. Tanaka, "Possibility of mutation prediction of influenza hemagglutinin by combination of hemadsorption experiment and quantum chemical calculation for antibody binding", J. Phys. Chem. B 113, 4991-4994 (2009).

N. Taguchi, Y. Mochizuki, T. Nakano, S. Amari, K. Fukuzawa, T. Ishikawa, M. Sakurai, S. Tanaka, "Fragment Molecular Orbital Calculations on Red Fluorescent Proteins (DsRed and mFruits)", J. Phys. Chem. B 113, 1153-1161 (2009).

Y. Okiyama, H. Watanabe, K. Fukuzawa, T. Nakano, Y. Mochizuki, T. Ishikawa, K. Ebina, S. Tanaka, "Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations", Chem. Phys. Lett. 467, 417-423 (2009).

T. Nakano, Y. Mochizuki, A. Kato, K. Fukuzawa, T. Ishikawa, S. Amari, I. Kurisaki, S. Tanaka, "Developments of FMO Methodology and Graphical User Interface in ABINIT-MP", in The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems, D. G. Fedorov, K. Kitaura, Eds.; pp.37-62, CRC Press, Boca Raton, FL, 2009.

Y. Mochizuki, T. Nakano, N. Taguchi, S. Tanaka, "Excited States of Photoactive Proteins by Configuration Interaction Studies", in The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems, D. G. Fedorov, K. Kitaura, Eds.; pp. 63-90, CRC Press, Boca Raton, FL, 2009.

K. Fukuzawa, Y. Mochizuki, T. Nakano, S. Tanaka, "Application of FMO Method to Specific Molecular Recognition of Biomacromolecules", in The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems, D. G. Fedorov, K. Kitaura, Eds.; pp. 133-170, CRC Press, Boca Raton, FL, 2009.

[2008]

M. Ito, K. Fukuzawa, Y. Mochizuki, T. Nakano, S. Tanaka, gAb Initio Fragment Molecular Orbital Study of Molecular Interactions between Liganded Retinoid X Receptor and Its Coactivator; Part II: Influence of Mutations in Transcriptional Activation Function 2 Activating Domain Core on the Molecular Interactionsh, J. Phys. Chem. A 112, 1986-1998 (2008).

M. Sato, H. Yamataka, Y. Komeiji, Y. Mochizuki, T. Ishikawa, T. Nakano, gHow Does an SN2 Reaction Take Place in Solution? Full Ab Initio MD Simulations for the Hydrolysis of the Methyl Diazonium Ionh, J. Am. Chem. Soc. 130, 2396-2397 (2008).

K. Koyano and T. Nakano, gInteraction of HIV-1 aspartic protease with its inhibitor, by molecular dynamics and ab initio fragment molecular orbital methodh, J. Synchrotron Rad. 15, 239242 (2008).

Y. Mochizuki, K. Yamashita, T. Murase, T. Nakano, K. Fukuzawa, K. Takematsu, H. Watanabe, S. Tanaka, gLarge scale FMO-MP2 calculations on a massively parallel-vector computerh, Chem. Phys. Lett. 457,  396-403 (2008).

T. Harada, K. Yamagishi, T. Nakano, K. Kitaura, H. Tokiwa, "Ab initio fragment molecular orbital study of ligand binding to human progesterone receptor ligand-binding domain", Naunyn-Schmiedeberg's Arch. Pharmac. 377, 607-615 (2008).

M. Ito, K. Fukuzawa, T. Ishikawa, Y. Mochizuki, T. Nakano, and S. Tanaka, gAb Initio Fragment Molecular Orbital Study of Molecular Interactions in Liganded Retinoid X Receptor: Specification of Residues Associated with Ligand Inducible Information Transmissionh, J. Phys. Chem. B, 112, 12081-12094 (2008).

T. Ishikawa, Y. Mochizuki, S. Amari, T. Nakano, S. Tanaka, K. Tanaka, gAn application of fragment interaction analysis based on local MP2h, Chem. Phys. Lett. 463, 189-194 (2008).

[2007]

Y. Komeiji, T. Ishikawa, Y. Mochizuki, H. Yamataka, T. Nakano, In "Computation in Modern Science and Engineering - Proc. ICCMSE2007 (T. E. Simos and G. Maroulis, eds, AIP)h, pp. 1261-1264 (2007).

Y. Okiyama, H. Watanabe, K. Fukuzawa, T. Nakano, Y. Mochizuki, T. Ishikawa, S. Tanaka, K. Ebina, gApplication of the fragment molecular orbital method for determination of atomic charges on polypeptidesh, Chem. Phys. Lett. 449, 329-335 (2007).

Y. Mochizuki, K. Tanaka, K. Yamashita, T. Ishikawa, T. Nakano, S. Amari, K. Segawa, T. Murase, H. Tokiwa, M. Sakurai, gParallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital schemeh, Theor. Chem. Acc. 117, 541-553 (2007).

Y. Mochizuki, T. Nakano, S. Amari, T. Ishikawa, K. Tanaka, M. Sakurai and S. Tanaka, gFragment molecular orbital calculations on red fluorescent protein (DsRed)h, Chem. Phys. Lett. 433, 360-367 (2007).

Y. Mochizuki, Y. Komeiji, T. Ishikawa, T. Nakano, H. Yamataka, gA fully quantum mechanical simulation study on the lowest np* state of hydrated formaldehydeh, Chem. Phys. Lett. 437, 66-72 (2007).

M. Ito, K. Fukuzawa, Y. Mochizuki, T. Nakano, and S. Tanaka, gAb Initio Fragment Molecular Orbital Study of Molecular Interactions between Liganded Retinoid X Receptor and Its Coactivator: Roles of Helix 12 in the Coactivator Binding Mechanismh, J. Phys. Chem. B 111, 3525-3533 (2007).

I. Kurisaki, K. Fukuzawa, Y. Komeiji, Y. Mochizuki, T. Nakano, J. Imada, A. Chmielewski, S. M. Rothstein, H. Watanabe, and S. Tanaka, gVisualization analysis of Inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital methodh, Biophys. Chem. 130, 1-9 (2007).

T. Ishikawa, Y. Mochizuki, S. Amari, T. Nakano, H. Tokiwa, S. Tanaka and K. Tanaka, gFragment interaction analysis based on local MP2h, Theor. Chem. Acc. 118, 937–945 (2007).

T. Watanabe, Y. Inadomi, K. Fukuzawa, T. Nakano, S. Tanaka, L. Nilsson, U. Nagashima, g DNA and Estrogen Receptor Interaction Revealed by Fragment Molecular Orbital Calculationsg, J. Phys. Chem. B 111, 9621-9627 (2007).