FMO references
1(1999)+1(2000)+1(2001)+2(2002)+4(2003)+7(2004)+10(2005)+17(2006)+20(2007)+
15(2008)+35(2009)+31(2010)+25(2011)+10(2012).

1. Fragment molecular orbital method: an approximate computational method 
for large molecules. K. Kitaura, E. Ikeo, T. Asada, T. Nakano, M.  Uebayasi,
Chem. Phys. Lett. 313 (1999) 701.

2. Fragment molecular orbital method: application to polypeptides.
T. Nakano, T. Kaminuma, T. Sato, Y. Akiyama, M. Uebayasi, K.  Kitaura, 
Chem. Phys. Lett. 318 (2000) 614.

3. Fragment molecular orbital method: analytical energy gradients. K.  Kitaura,
S.-I. Sugiki, T. Nakano, Y. Komeiji, M. Uebayasi, Chem. Phys.  Lett. 336 
(2001) 163.

4. Fragment molecular orbital method: use of approximate electrostatic
potential. T. Nakano, T. Kaminuma, T. Sato, K. Fukuzawa, Y. Akiyama,
M. Uebayasi, K. Kitaura, Chem. Phys. Lett. 351 (2002) 475.

5.  Definition of molecular orbitals in fragment molecular orbital method.
Y. Inadomi, T. Nakano, K. Kitaura, U. Nagashima, Chem. Phys.  Lett. 364 (2002)
139.

6. Fragment molecular orbital method: application to molecular dynamics 
simulation, 'ab initio FMO-MD'. Y. Komeiji, T. Nakano, K. Fukuzawa, Y. Ueno, 
Y. Inadomi, T. Nemoto, M. Uebayasi, D.G. Fedorov, K.  Kitaura, Chem. Phys. 
Lett. 372 (2003) 342.

7. Molecular orbital analysis based on fragment molecular orbital scheme.
H. Sekino, Y. Sengoku, S.-I. Sugiki and N. Kurita, Chem. Phys.  Lett. 378 
(2003) 589.

8. Fragment molecular orbital method with density functional theory and
DIIS convergence acceleration. S.-I. Sugiki, N. Kurita, Y. Sengoku and
H. Sekino, Chem. Phys. Lett. 382 (2003) 611.

9. Fragment molecular orbital study of the binding energy of ligands to the 
estrogen receptor. K. Fukuzawa, K. Kitaura, K. Nakata, T. Kaminuma, T. Nakano,
Pure Appl. Chem. 75 (2003) 2405-2410.

10. A new hierarchical parallelization scheme: generalized distributed
data interface (GDDI), and an application to the
fragment molecular orbital method (FMO). D. G. Fedorov, R. M. Olson,
K. Kitaura, M. S. Gordon, S. Koseki, J. Comput. Chem. 25 (2004) 872.

11. The importance of three-body terms in the fragment molecular orbital method.
D. G. Fedorov and K. Kitaura, J. Chem. Phys. 120 (2004) 6832.
 
12. Development of an ab initio MO-MD program based on fragment MO method: 
an attempt to analyze the fluctuation of protein. T. Ishimoto, H. Tokiwa, 
H. Teramae and U. Nagashima, Chem. Phys. Lett. 387 (2004) 460-465.

13. On the accuracy of the 3-body fragment molecular orbital method (FMO) 
applied to density functional theory. Dmitri G. Fedorov and Kazuo Kitaura,
Chem. Phys. Lett. 389 (2004) 129-134.

14. Second order Moeller-Plesset perturbation theory based upon the fragment 
molecular orbital method. D. G. Fedorov and K. Kitaura, J. Chem. Phys. 121 
(2004) 2483-2490.

15. Large scale MP2 calculations with fragment molecular orbital scheme.
Y. Mochizuki, S. Koikegami, T. Nakano, S. Amari and
K. Kitaura, Chem. Phys. Lett. 396 (2004) 473-479.

16. A parallelized integral-direct second-order Moeller-Plesset perturbation 
theory method with a fragment molecular orbital scheme. Y. Mochizuki, 
T. Nakano, S. Koikegami, S. Tanimori, Y. Abe, U. Nagashima and K. Kitaura,
Theor. Chem. Acc. 112 (2004) 442-452.

17. Ab initio quantum mechanical study of the binding energies of human 
estrogen receptor with its ligands: An application of fragment molecular 
orbital method. K. Fukuzawa, K. Kitaura, M. Uebayasi, K. Nakata, T. Kaminuma, 
T. Nakano, J. Comp. Chem. 26 (2005) 1-10.
 
18. Multiconfiguration self-consistent-field theory based upon the fragment 
molecular orbital method. D. G. Fedorov and K. Kitaura, J. Chem. Phys. 122
(2005) 054108.

19. Multilayer Formulation of the Fragment Molecular Orbital Method (FMO).
D. G. Fedorov, T. Ishida, K. Kitaura, J. Phys. Chem. A. 109 (2005) 2638-2646.

20. Theoretical study of intramolecular interaction energies during dynamics 
simulations of oligopeptides by the fragment molecular orbital-Hamiltonian 
algorithm method. T. Ishimoto, H. Tokiwa, H. Teramae, U. Nagashima, 
J. Chem. Phys. 122 (2005) 094905.

21. Configuration interaction singles method with multilayer fragment molecular
orbital scheme. Y. Mochizuki, S. Koikegami, S. Amari, K. Segawa, K. Kitaura and
T. Nakano, Chem. Phys. Lett. 406 (2005) 283-288.

22. A configuration analysis for fragment interaction. Y. Mochizuki, K. 
Fukuzawa, A. Kato, S. Tanaka, K. Kitaura and T. Nakano, Chem. Phys. Lett., 
410 (2005) 247-253.

23. Coupled-cluster theory based upon the fragment molecular-orbital method.
D. G. Fedorov and K. Kitaura, J. Chem. Phys. 123 (2005) 134103.

24. Density functional calculations on the interaction between catabolite 
activator protein and cyclic AMP using the fragment molecular orbital method.
S.-I. Sugiki, M. Matsuoka, R. Usuki, Y. Sengoku, N. Kurita, H. Sekino, 
S. Tanaka, J. Theor. Comp. Chem. 4 (2005) 183-195.

25. Full Electron Calculation Beyond 20,000 Atoms: Ground Electronic State of 
Photosynthetic Proteins. T. Ikegami, T. Ishida, D. G. Fedorov, K. Kitaura, 
Y. Inadomi, H. Umeda, M. Yokokawa, S. Sekiguchi,  Proc. of Supercomputing 2005,
IEEE Computer Society, 2005.
http://sc05.supercomputing.org/schedule/pdf/pap138.pdf

26. Ab initio fragment molecular orbital (FMO) method applied to analysis of 
the ligand-protein interaction in a pheromone-binding protein.
T. Nemoto, D. G. Fedorov, M. Uebayasi, K. Kanazawa, K. Kitaura, Y. Komeiji,
Comp. Biol. Chem. 29 (2005), 434.

27. All Electron Quantum Chemical Calculation of the Entire Enzyme System
Confirms a Collective Catalytic Device in the Chorismate Mutase Reaction.
T. Ishida, D. G. Fedorov, and K. Kitaura, J. Phys. Chem. B 110 (2006) 
1457-1463.

28. Dynamic polarizability calculation with fragment molecular orbital scheme.
Y. Mochizuki, T. Ishikawa, K. Tanaka, H. Tokiwa, T. Nakano, and S. Tanaka,
Chem. Phys. Lett. 418 (2006) 418-422.

29. A fragment molecular-orbital-multicomponent molecular-orbital
method for analyzing H/D isotope effects in large molecules.
T. Ishimoto, M. Tachikawa, U. Nagashima, J. Chem. Phys. 124 (2006) 014112.

30. VISCANA: Visualized Cluster Analysis of Protein-Ligand Interaction Based on
the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening.
S. Amari, M. Aizawa, J. Zhang,  K. Fukuzawa, Y. Mochizuki, Y. Iwasawa, K.
Nakata, H. Chuman, T. Nakano, J. Chem. Inf. Comput. Sci. 46 (2006) 221-230.

31. Functions of key residues in the ligand-binding pocket of vitamin D
receptor: Fragment molecular orbital-interfragment interaction energy
analysis. K. Yamagishi, K. Yamamoto, S. Yamada and H. Tokiwa, Chem. Phys. 
Lett. 420 (2006) 465-468.

32. Intra- and intermolecular interactions between cyclic-AMP receptor protein
and DNA: Ab initio fragment molecular orbital study. K. Fukuzawa, Y. Komeiji,
Y. Mochizuki, A. Kato, T. Nakano, S. Tanaka, J. Comp. Chem. 27 (2006)
948-960.

33. The polarizable continuum model (PCM) interfaced with the fragment 
molecular orbital method (FMO). D. G. Fedorov, K. Kitaura, H. Li, J. H. 
Jensen, M. S. Gordon, J. Comp. Chem. 27 (2006) 976-985.

34. Fragment molecular orbital calculations on large scale systems containing
heavy metal atom. T. Ishikawa, Y. Mochizuki, T. Nakano, S. Amari, H. Mori, 
H. Honda, T. Fujita, H. Tokiwa, S. Tanaka, Y. Komeiji, K. Fukuzawa, K. 
Tanaka, E. Miyoshi, Chem. Phys. Lett. 427 (2006) 159-165.

35. Theoretical development of the fragment molecular orbital (FMO) method.
D. G. Fedorov, K. Kitaura, in "Modern methods for theoretical physical 
chemistry of biopolymers", E. B. Starikov, J. P. Lewis, S. Tanaka, Eds.,
pp 3-38, Elsevier, Amsterdam, 2006. 

36. Developments and applications of ABINIT-MP software based on the fragment 
molecular orbital method. T. Nakano, Y. Mochizuki, K. Fukuzawa, S. Amari, S. 
Tanaka, in "Modern methods for theoretical physical chemistry of biopolymers", 
E. B. Starikov, J. P. Lewis, S. Tanaka, Eds., pp 39-52, Elsevier, Amsterdam, 
2006.

37. Molecular Interactions between Estrogen Receptor and Its Ligand Studied by
the ab Initio Fragment Molecular Orbital Method. K. Fukuzawa, Y. Mochizuki, 
S. Tanaka, K. Kitaura, T. Nakano, J. Phys. Chem. B 110 (2006) 16102-16110.

38. Examination of numerical accuracy on fragment-DFT calculations with
integral values of total electron density functions. Y. Shimodo, K. Morihashi
and T. Nakano, J. Mol. Str. (THEOCHEM), 770 (2006) 163-168.

39. Application of fragment molecular orbital scheme to silicon-containing
systems. T. Ishikawa, Y. Mochizuki, K. Imamura, T. Nakano, H. Mori, H. Tokiwa,
K. Tanaka, E. Miyoshi, S. Tanaka, Chem. Phys. Lett. 430 (2006) 361-366.

40. The extension of the fragment molecular orbital method with the
many-particle Green's function. K. Yasuda, D. Yamaki, J. Chem. Phys. 125
(2006) 154101.

41. Why does avian influenza A virus hemagglutinin bind to avian receptor
stronger than to human receptor? Ab initio fragment molecular orbital
studies. T. Sawada, T. Hashimoto, H. Nakano, T. Suzuki, H. Ishida, M. Kiso,
Biochem. Biophys. Res. Comm. 351 (2006) 40-43.

42. The three-body fragment molecular orbital method for accurate calculations
of large systems. D. G. Fedorov, K. Kitaura, Chem. Phys. Lett. 433 (2006) 
182-187.

43. Ab initio biomolecular calculations using quantum Monte Carlo combined
with the fragment molecular orbital method. R. Maezono, H. Watanabe, S. Tanaka,
in Advances in Quantum Monte Carlo, J. B. Anderson, S. M. Rothstein, Eds., 
ACS Symposium Series 953, pp 141-146, American Chemical Society:
Washington, DC, 2006.

44. Pair interaction energy decomposition analysis. D. G. Fedorov, K. Kitaura,
J. Comp. Chem. 28 (2007) 222-237.

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

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

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

48. Ab 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. M. Ito, K. Fukuzawa, Y. Mochizuki, 
T. Nakano, S. Tanaka, J. Phys. Chem. B 111 (2007) 3525-3533. 

49. Influenza viral hemagglutinin complicated shape is advantageous to its 
binding affinity for sialosaccharide receptor. T. Sawada, T. Hashimoto, 
H. Nakano, T. Suzuki, Y. Suzuki, Y. Kawaoka, H. Ishida, M. Kiso, 
Biochem. Biophys. Res. Comm. 355 (2007) 6-9.

50. The Fragment Molecular Orbital Method for Geometry Optimizations of
Polypeptides and Proteins. D. G. Fedorov, T. Ishida, M. Uebayasi, K. Kitaura, 
J. Phys. Chem. A 111 (2007) 2722-2732.

51. Accuracy of the three-body fragment molecular orbital method applied to
Moeller-Plesset perturbation theory. D. G. Fedorov, K. Ishimura, T. Ishida, 
K. Kitaura, P. Pulay, S. Nagase, J. Comp. Chem. 28 (2007) 1476-1484.

52. Molecular recognition mechanism of FK506 binding protein: An all-electron
fragment molecular orbital study. I. Nakanishi, D. G. Fedorov, K. Kitaura, 
Proteins: Struct., Funct., Bioinf. 68 (2007) 145-158.

53. Change in a protein's electronic structure induced by an explicit solvent:
An ab initio fragment molecular orbital study of ubiquitin. Y. Komeiji,
T. Ishida, D. G. Fedorov, K. Kitaura, J. Comp. Chem. 28 (2007) 1750-1762.

54. Extending the Power of Quantum Chemistry to Large Systems with the
Fragment Molecular Orbital Method. D. G. Fedorov, K. Kitaura, J. Phys. 
Chem. A 111 (2007) 6904-6914.

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

56. Ab initio study of molecular interactions in higher plant and Galdieria
partita Rubiscos with the fragment molecular orbital method. H. Watanabe, T. 
Enomoto, S. Tanaka, Biochem. Biophys. Res. Comm. 361 (2007) 367-372.

57. Time-dependent density functional theory with the multilayer fragment
molecular orbital method. M. Chiba, D. G. Fedorov, K. Kitaura, Chem. Phys. 
Lett. 444 (2007) 346-350.

58. Ab initio NMR chemical shift calculations on proteins using fragment
molecular orbitals with electrostatic environment. Q. Gao, S. Yokojima,
T. Kohno, T. Ishida, D. G. Fedorov, K. Kitaura, M. Fujihira, S. Nakamura,
Chem. Phys. Lett. 445 (2007) 331-339.

59. Time-dependent density functional theory based upon the fragment molecular
orbital method. M. Chiba, D. G. Fedorov, K. Kitaura, J. Chem. Phys. 127 (2007)
104108.

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

61. Fragment interaction analysis based on local MP2.
T. Ishikawa, Y. Mochizuki, S. Amari, T. Nakano, H. Tokiwa, S. Tanaka, K. Tanaka,
Theor. Chem.  Acc. 118 (2007) 937-945.

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

63. Fragmentation Method Combined with Quantum Monte Carlo Calculations.
R. Maezono, H. Watanabe, S. Tanaka, M. D. Towler, R. J. Needs,
J. Phys. Soc. Jap. 76 (2007) 064301.

64. Receptor-specific scoring functions derived from quantum chemical models 
improve affinity estimates for in-silico drug discovery.
B. Fischer, K. Fukuzawa, W. Wenzel, Proteins: Struct., Funct., Bioinf. 70 
(2008) 1264-1273.

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

66. Ab 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. M. Ito, K. Fukuzawa, Y. Mochizuki, T. Nakano, 
S. Tanaka, J. Phys. Chem. A 112 (2008) 1986-1998.

67. Theoretical analysis of binding specificity of influenza viral
hemagglutinin to avian and human receptors based on the fragment molecular
orbital method. T. Iwata, K. Fukuzawa, K. Nakajima, S. Aida-Hyugaji,
Y. Mochizuki, H. Watanabe, S. Tanaka, Comput. Biol. Chem. 32 (2008) 198-211.

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

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

70. QSAR Study of Cyclic Urea Type HIV-1 PR Inhibitors Using Ab
Initio MO Calculation of Their Complex Structures with HIV-1.
T. Yoshida, K. Yamagishi, H. Chuman, QSAR Comb. Sci. 27 (2008) 694-703.

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

72. CH/pi hydrogen bonds determine the selectivity of the Src homology 2
domain to tyrosine phosphotyrosyl peptides: An ab initio fragment molecular
orbital study. T. Ozawa, K. Okazaki, J. Comp. Chem. 29 (2008) 2656-2666.

73. Polarizable continuum model with the fragment molecular orbital-based
time-dependent density functional theory. M. Chiba, D. G. Fedorov, K. Kitaura, 
J. Comp. Chem. 29 (2008) 2667-2676.

74. Theoretical Analysis of the Intermolecular Interaction Effects on the
Excitation Energy of Organic Pigments: Solid State Quinacridone.
H. Fukunaga, D. G. Fedorov, M. Chiba, K. Nii, K. Kitaura, J. Phys. Chem. A 
112 (2008) 10887-10894.

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

76. Covalent Bond Fragmentation Suitable To Describe Solids in the Fragment
Molecular Orbital Method. D. G. Fedorov, J. H. Jensen, R. C. Deka, K. Kitaura,
J. Phys. Chem. A 112 (2008) 11808-11816.

77. The importance of CH/pi hydrogen bonds in rational drug design: An ab
initio fragment molecular orbital study to leukocyte-specific protein tyrosine
(LCK) kinase, T. Ozawa, E. Tsuji, M. Ozawa, C. Handa, H. Mukaiyama, T. 
Nishimura, S. Kobayashi, K. Okazaki, Bioorg. Med. Chem. 16 (2008), 10311-10318.

78. Ab initio fragment molecular orbital studies of influenza virus 
hemagglutinin-sialosaccharide complexes toward chemical clarification about 
the virus host range determination. T. Sawada, T. Hashimoto, H. Tokiwa, T.
Suzuki, H. Nakano, H. Ishida, M. Kiso, Y. Suzuki, Glycoconj. J. 25 (2008) 
805-815.

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

80. 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. Y. Okiyama, H. Watanabe, 
K. Fukuzawa, T. Nakano, Y. Mochizuki, T. Ishikawa, K. Ebina, S. Tanaka,
Chem. Phys. Lett. 467 (2009) 417-423.

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

82. Ab initio fragment molecular orbital (FMO) analysis of the structure of the
phosphoinositide-binding peptide from gelsolin. M. Tada, T. Nagasima, T. 
Udagawa, M. Tachikawa, H. Sugawara J. Mol. Str. (THEOCHEM) 897 (2009) 149-153.

83. Fragment molecular orbital-based molecular dynamics (FMO-MD), a quantum
simulation tool for large molecular systems. Y. Komeiji, Y. Mochizuki, T.
Nakano, D. G. Fedorov, J. Mol. Str. (THEOCHEM) 898 (2009) 2-7.

84. Ab initio quantum-chemical study on emission spectra of bioluminescent
luciferases by fragment molecular orbital method. A. Tagami, N. Ishibashi, 
D. Kato, N. Taguchi, Y. Mochizuki, H. Watanabe, M. Ito, S. Tanaka,
Chem. Phys. Lett. 472 (2009) 118-123.

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

86. Importance of dispersion and electron correlation in ab initio protein
folding. X. He, L. Fusti-Molnar, G. Cui, K. M. Merz, Jr., J. Phys. Chem. B
113 (2009) 5290-5300.

87. Structural and interaction analysis of helical heparin oligosaccharides
with the fragment molecular orbital method. T. Sawada, D. G. Fedorov, K.
Kitaura, Int. J. Quant. Chem. 109 (2009) 2033-2045.

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

89. Novel Quantitative Structure-Activity Studies of HIV-1 Protease Inhibitors
of the Cyclic Urea Type Using Descriptors Derived from Molecular Dynamics and 
Molecular Orbital Calculations. T. Yoshida, T. Fujita, H. Chuman,
Curr. Comp.-Aided Drug Des. 5 (2009) 38-55.

90. Fragment molecular orbital calculation using the RI-MP2 method.
T. Ishikawa, K. Kuwata, Chem. Phys. Lett. 474 (2009) 195-198.

91. Excited state geometry optimizations by time-dependent density functional
theory based on the fragment molecular orbital method. M. Chiba, D. G. Fedorov,
T. Nagata, K. Kitaura, Chem. Phys. Lett. 474 (2009) 227-232.

92. Theoretical Background of the Fragment Molecular Orbital (FMO) Method
and Its Implementation in GAMESS. D. G. Fedorov, K. Kitaura, in The Fragment
Molecular Orbital Method: Practical Applications to Large Molecular Systems,
D. G. Fedorov, K. Kitaura, Eds.; pp. 5-36, CRC Press, Boca Raton, FL, 2009.

93. Developments of FMO Methodology and Graphical User Interface in
ABINIT-MP. T. Nakano, Y. Mochizuki, A. Kato, K. Fukuzawa, T. Ishikawa, S.
Amari, I. Kurisaki, S. Tanaka, 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.

94. Excited States of Photoactive Proteins by Configuration Interaction
Studies. Y. Mochizuki, T. Nakano, N. Taguchi, S. Tanaka, 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.

95. The Fragment Molecular Orbital - Based Time-Dependent Density Functional
Theory for Excited States in Large Systems. M. Chiba, D. G. Fedorov, K.
Kitaura, in The Fragment Molecular Orbital Method: Practical Applications to
Large Molecular Systems, D. G. Fedorov, K. Kitaura, Eds.; pp. 91-118, CRC
Press, Boca Raton, FL, 2009.

96. FMO-MD An ab initio-Based Molecular Dynamics of Large Systems. Y.
Komeiji, in The Fragment Molecular Orbital Method: Practical Applications to
Large Molecular Systems, D. G. Fedorov, K. Kitaura, Eds.; pp. 119-132.

97. Application of FMO Method to Specific Molecular Recognition of
Biomacromolecules, by K. Fukuzawa, Y. Mochizuki, T. Nakano, S. Tanaka, 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.

98. Detailed Electronic Structure Studies Revealing the Nature of
Protein-Ligand Binding. I. Nakanishi, D. G. Fedorov, K. Kitaura, in The
Fragment Molecular Orbital Method: Practical Applications to Large Molecular
Systems, D. G. Fedorov, K. Kitaura, Eds.; pp. 171-192, CRC Press, Boca Raton,
FL, 2009.

99. How Does FMO Method Help in Studying Viruses and Their Binding to
Receptors? T. Sawada, T. Hashimoto, H. Tokiwa, T. Suzuki, H. Nakano, H.
Ishida, M. Kiso, Y. Suzuki, in The Fragment Molecular Orbital Method:
Practical Applications to Large Molecular Systems, D. G. Fedorov, K.
Kitaura, Eds.; pp. 193-216, CRC Press, Boca Raton, FL, 2009.

100. FMO as a Tool for Structure-Based Drug Design. T. Ozawa, K. Okazaki, M.
Nishio, in The Fragment Molecular Orbital Method: Practical Applications to
Large Molecular Systems, D. G. Fedorov, K. Kitaura, Eds.; pp. 217-244, CRC
Press, Boca Raton, FL, 2009.

101. Modeling Protein Environment in an Enzymatic Catalysis A Case Study of
the Chorismate Mutase Reaction, T. Ishida, in The Fragment Molecular Orbital
Method: Practical Applications to Large Molecular Systems, D. G. Fedorov, K.
Kitaura, Eds.; pp. 245-268, CRC Press, Boca Raton, FL, 2009.

102. Derivatives of the approximated electrostatic potentials in the fragment
molecular orbital method. T. Nagata, D. G. Fedorov, K. Kitaura,
Chem. Phys. Lett. 475 (2009) 124-131.

103. Molecular orbital calculation of biomolecules with fragment molecular
orbitals. S. Tsuneyuki, T. Kobori, K. Akagi, K. Sodeyama, K. Terakura, H. 
Fukuyama, Chem. Phys. Lett. 476 (2009) 104-108.

104. A combined effective fragment potential - fragment molecular orbital 
method. I. The energy expression and initial applications.
T. Nagata, D. G. Fedorov, K. Kitaura, M. S. Gordon, J. Chem. Phys. 131 
(2009) 024101.

105. Analytic gradient for the adaptive frozen orbital bond detachment
in the fragment molecular orbital method. D. G. Fedorov, P. V. Avramov, 
J. H. Jensen, K. Kitaura, Chem. Phys. Lett. 477 (2009) 169-175.

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

107. Ab initio molecular orbital calculations on specific interactions between
urokinase-type plasminogen activator and its receptor. K. Nagase, H. Kobayashi,
E. Yoshikawa, N. Kurita, J. Mol. Graph. Mod. 28 (2009) 46-53.

108. A combined simulation with ab initio MO and classical vibrational
analysis on the specific interactions between thermolysin and dipeptide 
ligands. K. Dedachi, M. T. H. Khan, I. Sylte, N. Kurita, Chem. Phys. Lett. 
479 (2009) 290-295.

109. Roles of K151 and D180 in L-2-haloacid dehalogenase from Pseudomonas
sp. YL: Analysis by molecular dynamics and ab initio fragment molecular
orbital calculations. T. Nakamura, A. Yamaguchi, H. Kondo, H. Watanabe, T.
Kurihara, N. Esaki, S. Hirono, S. Tanaka, J. Comp. Chem. 30 (2009) 2625-2634.

110. Theoretical study of the prion protein based on the fragment molecular 
orbital method. T. Ishikawa, T. Ishikura, K. Kuwata, J. Comp. Chem. 30 (2009) 
2594-2601.

111. Ab initio path integral molecular dynamics based on fragment molecular 
orbital method. T. Fujita, H. Watanabe, S. Tanaka, J. Phys. Soc. Jap. 78 (2009)
104723.

112. Solvatochromic Shifts of Uracil and Cytosine Using a Combined
Multireference Configuration Interaction/Molecular Dynamics Approach and the
Fragment Molecular Orbital Method. K. A. Kistler, S. Matsika, J. Phys. Chem. A
113 (2009) 12396-12403.

113. The role of the exchange in the embedding electrostatic potential for the
fragment molecular orbital method. D. G. Fedorov, K. Kitaura, J. Chem. Phys. 
131 (2009) 171106.

114. Fragment molecular orbital study of the electronic excitations in the
photosynthetic reaction center of Blastochloris viridis. T. Ikegami, T. Ishida,
D. G. Fedorov, K. Kitaura, Y. Inadomi, H. Umeda, M. Yokokawa, S. Sekiguchi,
J. Comp. Chem. 31 (2010) 447-454.

115. Three-body expansion and generalized dynamic fragmentation improve the
fragment molecular orbital-based molecular dynamics (FMO-MD).
Y. Komeiji, Y. Mochizuki, T, Nakano, Chem. Phys. Lett. 484 (2010) 380-386.

116. Open-Shell Formulation of the Fragment Molecular Orbital Method.
S. R. Pruitt, D. G. Fedorov, K. Kitaura, M. S. Gordon, J. Chem. Theory Comp.
6 (2010) 1-5.

117. Energy gradients in combined fragment molecular orbital and
polarizable continuum model (FMO/PCM) calculation. H. Li, D. G. Fedorov, 
T. Nagata, K. Kitaura, J. H. Jensen, M. S. Gordon, J. Comp. Chem. 
31 (2010) 778-790.

118. Interaction Analysis of the Native Structure of Prion Protein with
Quantum Chemical Calculations. T. Ishikawa, K. Kuwata, J. Chem. Theory Comp.
6 (2010) 538-547.

119. Multivariate analysis of properties of amino acid residues in proteins
from a viewpoint of functional site prediction. S. Du, M. Sakurai, Chem. Phys. 
Lett. 488 (2010) 81-85.

120. Nuclear-Electronic Orbital Method within the Fragment Molecular Orbital
Approach. B. Auer, M. V. Pak, S. Hammes-Schiffer, J. Phys. Chem. C 114 (2010)
5582-5588.

121. Molecular mechanics and all-electron fragment molecular orbital
calculations on mutated polyglutamine peptides. B. M. B. Van Schouwen, M.
Nakano, H. Watanabe, S. Tanaka, H. L. Gordon, S. M. Rothstein,  J. Mol. Str.
(THEOCHEM) 944 (2010) 12-20.

122. Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations
on hydrated Zn(II) ion. T. Fujiwara, Y. Mochizuki, Y. Komeiji, Y. Okiyama, 
H. Mori, T. Nakano, E. Miyoshi, Chem. Phys. Lett. 490 (2010) 41-45.

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

124. Fragment-Molecular-Orbital-Method-Based ab Initio NMR Chemical-Shift
Calculations for Large Molecular Systems. Q. Gao, S. Yokojima, D. G. Fedorov, 
K. Kitaura, M. Sakurai, S. Nakamura, J. Chem. Theory Comp. 6 (2010), 1428-1444.

125. Flexible ligand recognition of peroxisome proliferator-activated
receptor-gamma (PPARgamma). K. Yamagishi, K. Yamamoto, Y. Mochizuki, 
T. Nakano, S. Yamada, H. Tokiwa, Bioorg. Med. Chem. Lett. 20 (2010) 3344-3347.

126. Correlation analyses on binding affinity of Substituted benzenesulfonamides
with carbonic anhydrase using ab initio MO calculations on their Complex
structures. T. Yoshida, Y. Munei, S. Hitaoka, H. Chuman, J. Chem. Inf. Model. 
50 (2010) 850-860.

127. Importance of the hybrid orbital operator derivative term for the energy
gradient in the fragment molecular orbital method. T. Nagata, D. G. Fedorov, 
K. Kitaura, Chem. Phys. Lett. 492 (2010) 302-308.

128. Does amination of formaldehyde proceed through a zwitterionic
intermediate in water? Fragment molecular orbital molecular dynamics
simulations by using constraint dynamics. M. Sato, H. Yamataka, Y. Komeiji, 
Y. Mochizuki, T. Nakano, Chem. Eur. J. 16 (2010) 6430-6433.

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

130. Ligand-dependent conformation change reflects steric structure and
interactions of a vitamin D receptor/ligand complex: a fragment molecular
orbital study. S. Motoyoshi, K. Yamagishi, S. Yamada, H. Tokiwa,
J. Ster. Biochem. Mol. Biol. 121 (2010) 56-59.

131. Interactions between 1alpha,25(OH)2D3 and residues in the ligand-binding 
pocket of the vitamin D receptor: a correlated fragment molecular orbital 
study. K. Yamagishi, H. Tokiwa, M. Makishima, S. Yamada, J. Ster. Biochem. Mol.
Biol. 121 (2010) 63-67.

132. Systematic Study of the Embedding Potential Description in the Fragment
Molecular Orbital Method. D. G. Fedorov, L. V. Slipchenko, K. Kitaura,
J. Phys. Chem. A 114 (2010) 8742-8753.

133. Parallel Fock matrix construction with distributed shared memory model
for the FMO-MO method. H. Umeda, Y. Inadomi, T. Watanabe, T. Yagi, T. Ishimoto,
T. Ikegami, H. Tadano, T. Sakurai, U. Nagashima, J. Comp. Chem. 31 (2010) 
2381-2388.

134. Electronic excitation energy calculation by the fragment molecular orbital
method with three-body effects. M. Chiba, T. Koido, J. Chem. Phys. 133 (2010) 
044113.

135. Specific interactions between aryl hydrocarbon receptor and dioxin
congeners: Ab initio fragment molecular orbital calculations. E. Yoshikawa, 
S. Miyagi, K. Dedachi, M. Ishihara-Sugano, S. Itoh, N. Kurita, J. Mol. Graph. 
Mod. 29 (2010) 197-205.

136. The role of fluorine atoms in a fluorinated prostaglandin agonist.
K. Fujimura, Y. Sasabuchi, Chem. Med. Chem. 5 (2010) 1254-1257.

137. Incorporation of solvation effects into the fragment molecular orbital
calculations with the Poisson-Boltzmann equation. H. Watanabe, Y. Okiyama, 
T. Nakano, S. Tanaka, Chem. Phys. Lett. 500 (2010) 116-119.

138. Partial energy gradient based on the fragment molecular orbital method:
Application to geometry optimization. T. Ishikawa, N. Yamamoto, K. Kuwata,
Chem. Phys. Lett. 500 (2010) 149-154.

139. Fragment molecular orbital investigation of the role of AMP protonation in
firefly luciferase pH-sensitivity. B. F. Milne, M. A. L. Marques, F. Nogueira,
Phys. Chem. Chem. Phys. 12 (2010) 14285-14293.

140. Correlation analyses on binding affinity of sialic acid analogues with
influenza virus neuraminidase-1 using ab initio MO calculations on their
complex structures. S. Hitaoka, M. Harada, T. Yoshida, H. Chuman,
J. Chem. Inf. Model. 50 (2010) 1796-1805.

141. Role of the key mutation in the selective binding of avian and human
influenza hemagglutinin to sialosides revealed by quantum-mechanical
calculations. T. Sawada, D. G. Fedorov, K. Kitaura, J. Am. Chem. Soc. 132 
(2010) 16862-16872.

142. Binding of influenza A virus hemagglutinin to the sialoside receptor is
not controlled by the homotropic allosteric effect. T. Sawada, D. G. Fedorov, 
K. Kitaura, J. Phys. Chem. B 114 (2010) 15700-15705.

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

144. Hasegawa, K.; Mohri, S.; Yokoyama, T. Fragment molecular orbital
calculations reveal that the E200K mutation markedly alters local structural
stability in the human prion protein. Prion 4 (2010) 38-44.

145. Correlation analyses on binding affinity of substituted 
benzenesulfonamides with carbonic anhydrase using ab initio MO calculations on
their complex structures (II). Y. Munei, K. Shimamoto, M. Harada, T. Yoshida, 
H. Chuman, Bioorg. Med. Chem. Lett. 21 (2011) 141-144.

146. Computational Insights into Binding of Bisphosphates to Farnesyl
Pyrophosphate Synthase. K. Ohno, K. Mori, M. Orita, M. Takeuchi,
Curr. Med. Chem. 18 (2011) 220-233.

147. A combined effective fragment potential - fragment molecular orbital 
method. II. Analytic gradient and application to the geometry optimization of
solvated tetraglycine and chignolin. T. Nagata, D. G. Fedorov, T. Sawada,
K. Kitaura, M. S. Gordon, J. Chem. Phys. 134 (2011) 034110.

148. Geometry optimization of the active site of a large system with the
fragment molecular orbital method. D. G. Fedorov, Y. Alexeev, K. Kitaura,
J. Phys. Chem. Lett. 2 (2011) 282-288.

149. Fragment molecular orbital calculations for excitation energies of blue- 
and yellow-fluorescent proteins. N. Taguchi, Y. Mochizuki, T. Nakano, Chem. 
Phys. Lett. 504 (2011) 76-82.

150. Fragment molecular orbital-based molecular dynamics (FMO-MD) method with 
MP2 gradient. Y. Mochizuki, T. Nakano, Y. Komeiji, K. Yamashita, Y. Okiyama, 
H. Yoshikawa, H. Yamataka, Chem. Phys. Lett. 504 (2011) 95-99.

151. Fully analytic energy gradient in the fragment molecular orbital method.
T. Nagata, K. Brorsen, D. G. Fedorov, K. Kitaura, M. S. Gordon, J. Chem. 
Phys. 134 (2011) 124115.

152. Mathematical Formulation of the fragment molecular orbital method.
T. Nagata, D. G. Fedorov, K. Kitaura. In Linear-Scaling Techniques
in Computational Chemistry and Physics. R. Zalesny, M. G. Papadopoulos,
P. G. Mezey, J. Leszczynski (Eds.), Springer, New York, 2011, pp. 17-64.

153. Specific interactions between lactose repressor protein and DNA affected 
by ligand binding: Ab initio molecular orbital calculations. T. Ohyama, 
M. Hayakawa, S. Nishikawa, N. Kurita, J. Comp. Chem. 32 (2011) 1661-1670. 

154. Fragment molecular orbital calculations under periodic boundary condition.
T. Fujita, T. Nakano, S. Tanaka, Chem. Phys. Lett. 506 (2011) 112-116.

155. A theoretical study of the Physicochemical Mechanisms Associated with DNA
Recognition Modulation in Artificial Zinc-Finger Proteins. H. Mori, K. 
Ueno-Noto, J. Phys. Chem. B 115 (2011) 4774-4780.

156. The effects of amino-acid mutations on specific interactions between
urokinase-type plasminogen activator and its receptor: Ab initio molecular
orbital calculations. S. Tsuji, T. Kasumi, K. Nagase, E. Yoshikawa, H. 
Kobayashi, N. Kurita, J. Mol. Graph. Mod. 29 (2011) 975-984.

157. Counterpoise-corrected interaction energy analysis based on the fragment
molecular orbital scheme. Y. Okiyama, K. Fukuzawa, H. Yamada, Y. Mochizuki, 
T. Nakano, S. Tanaka, Chem. Phys. Lett. 509 (2011) 67-71.

158. Sialic Acid Recognition of the Pandemic Influenza 2009 H1N1 Virus:
Binding Mechanism Between Human Receptor and Influenza Hemagglutinin.
K. Fukuzawa, K. Omagari, K. Nakajima, E. Nobusawa, S. Tanaka, Prot. Pept. 
Lett. 18 (2011) 530-539.

159. The role of intermolecular hydrogen bond on dielectric properties in
hydrogen-bonded material 5-bromo-9-hydroxyphenalenone: theoretical
investigation. H. Otaki, K. Ando, Phys. Chem. Chem. Phys. 13 (2011) 10719-10728.

160. Electronic coupling calculation and pathway analysis of electron transfer
reaction using ab initio fragment-based method. I. FMO-LCMO approach.
H. Nishioka, K. Ando, J. Chem. Phys. 134 (2011) 204109.

161. Analytic energy gradient for second-order Moeller-Plesset perturbation
theory based on the fragment molecular orbital method. T. Nagata, D. G. Fedorov,
K. Ishimura, K. Kitaura, J. Chem. Phys. 135 (2011) 044110.

162. Importance of CH/pi Hydrogen Bonds in Recognition of the
Core Motif in Proline-Recognition Domains: An Ab Initio
Fragment Molecular Orbital Study. T. Ozawa, K. Okazaki, K. Kitaura,
J. Comput. Chem. 32 (2011) 2774-2782.

163. CH/pi hydrogen bonds play a role in ligand recognition and equilibrium
between active and inactive states of the b2 adrenergic receptor:
An ab initio fragment molecular orbital (FMO) study.
T. Ozawa, K. Okazaki, K. Kitaura. Bioorg. Med. Chem. 19 (2011) 5231-5237.

164. Prediction of probable mutations in influenza virus hemagglutinin protein
based on large-scale ab initio fragment molecular orbital calculations.
A. Yoshioka, K. Fukuzawa, Y. Mochizuki, K. Yamashita, T. Nakano, Y. Okiyama, 
E. Nobusawa, K. Nakajima, S. Tanaka, J. Mol. Graph. Mod. 30 (2011) 110-119.

165. Correlation Analyses on Binding Affinity of Sialic Acid Analogues and
Anti-Influenza Drugs with Human Neuraminidase Using ab Initio MO Calculations
on Their Complex Structures ? LERE-QSAR Analysis (IV). S. Hitaoka, H. Matoba,
M. Harada, T. Yoshida, D. Tsuji, T. Hirokawa, K. Itoh,  H. Chuman, J. Chem.
Inf. Model. 2011, 51, 2706-2716.

166. Evolution of amide stacking in larger gamma-peptides: triamide H-bonded
cycles. W. H. James III, E. G. Buchanan, C. W. Mueller, J. C. Dean, 
D. Kosenkov, L. V. Slipchenko, L. Guo, A. G. Reidenbach, S. H. Gellman, 
T. S. Zwier, J. Phys. Chem. A 115 (2011) 13783-13798.

167. Application of resolution of identity approximation of second-order
Moeller-Plesset perturbation theory to three-body fragment molecular orbital
method. M. Katouda, Theor. Chem. Acc. 130 (2011) 449-453.

168. Higher-order correlated calculations based on fragment molecular orbital
scheme. Y. Mochizuki, K. Yamashita, T. Nakano, Y. Okiyama, K. Fukuzawa, 
N. Taguchi, S. Tanaka, Theor. Chem. Acc. 130 (2011) 515-530.

169. Antigen-antibody interactions of influenza virus hemagglutinin revealed by 
the fragment molecular orbital calculation. A. Yoshioka, K. Takematsu, 
I. Kurisaki, K. Fukuzawa, Y. Mochizuki, T. Nakano, E. Nobusawa, K. Nakajima, 
S. Tanaka, Theor. Chem. Acc. 130 (2011) 1197-1202.

170. Large-Scale MP2 Calculations on the Blue Gene Architecture Using the
Fragment Molecular Orbital Method. G. D. Fletcher, D. G. Fedorov, S. R.
Pruitt, T. L. Windus, M. S. Gordon, J. Chem. Theory Comput. 8 (2012) 75-79.

171. Specific interactions and binding energies between thermolysin and potent
inhibitors: Molecular simulations based on ab initio molecular orbital method.
T. Hirakawa, S. Fujita, T. Ohyama, K. Dedachi, M. Tareq, H. Khan, I. Sylte, 
N. Kurita, J. Mol. Graph. Mod. 33 (2012) 1-11

172. Development of the four-body corrected fragment molecular orbital (FMO4)
method. T. Nakano, Y. Mochizuki, K. Yamashita, C. Watanabe, K. Fukuzawa, 
K. Segawa, Y. Okiyama, T. Tsukamoto, S. Tanaka, Chem. Phys. Lett. 523 (2012) 
128-133.

173. Large-scale ab initio calculations of archetypical ionic liquids. E. I. 
Izgorodina, J. Rigby, D. R. MacFarlane, Chem. Commun. 48 (2012) 1493-1495.

174. Energy decomposition analysis in solution based on the fragment
molecular orbital method. D. G. Fedorov, K. Kitaura, J. Phys. Chem. A 116 (2012)
704-719.

175. RI-MP2 gradient calculation of large molecules using the fragment
molecular orbital method. T. Ishikawa, K. Kuwata, J. Phys. Chem. Lett. 3 (2012)
375-379.

176. Analytic gradient and molecular dynamics simulations using the fragment
molecular orbital method combined with effective potentials. T. Nagata, 
D. G. Fedorov, K. Kitaura, Theor. Chem. Acc. 131 (2012) 1136.

177. Differences in hydration between cis- and trans-platin: Quantum insights
by ab initio fragment molecular orbital-based molecular dynamics (FMO-MD).
H. Mori, N. Hirayama, Y. Komeiji, Y. Mochizuki, Comp. Theor. Chem. 986 (2012) 
30-34.

178. Partial geometry optimization with FMO-MP2 gradient: Application to
TrpCage. T. Tsukamoto, Y. Mochizuki, N. Watanabe, K. Fukuzawa, T. Nakano,
Chem. Phys. Lett. 535 (2012) 157-162.

179. Exploring chemistry with the fragment molecular orbital method. D. G. 
Fedorov, T. Nagata, K. Kitaura, Phys. Chem. Chem. Phys. 14 (2012) 7562-7577.