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)+26(2011)+27(2012)+18(2013)+24(2014)+19(2015)+
17(2016)+22(2017)+28(2018)+21(2019)+34(2020)+52(2021)+27(2022)+21(2023)+
7(2024).

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for large molecules. K. Kitaura, E. Ikeo, T. Asada, T. Nakano, M. Uebayasi,
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2. Fragment molecular orbital method: application to polypeptides.
T. Nakano, T. Kaminuma, T. Sato, Y. Akiyama, M. Uebayasi, K. Kitaura, 
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3. Fragment molecular orbital method: analytical energy gradients. K. Kitaura, 
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163-170.

4. Fragment molecular orbital method: use of approximate electrostatic
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5.  Definition of molecular orbitals in fragment molecular orbital method.
Y. Inadomi, T. Nakano, K. Kitaura, U. Nagashima, Chem. Phys. Lett. 364 (2002)
139-143.

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. 
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7. Molecular orbital analysis based on fragment molecular orbital scheme.
H. Sekino, Y. Sengoku, S.-I. Sugiki, N. Kurita, Chem. Phys.  Lett. 378 
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8. Fragment molecular orbital method with density functional theory and
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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. Comp. Chem. 25 (2004) 872-880.

11. The importance of three-body terms in the fragment molecular orbital 
method. D. G. Fedorov, K. Kitaura, J. Chem. Phys. 120 (2004) 6832-6840.

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, 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. D. G. Fedorov, K. 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, 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, 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, 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, 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.
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, T. Nakano, Chem. Phys. Lett.
410 (2005) 247-253.

23. Coupled-cluster theory based upon the fragment molecular-orbital method.
D. G. Fedorov, 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) 434-439.

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, 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, 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. Comp. 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, 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, Comp. 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. Comp. 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. 51 (2011) 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. Prediction of cyclin-dependent kinase 2 inhibitor potency using the
fragment molecular orbital method. M. P. Mazanetz, O. Ichihara, R. J. Law,
M. Whittaker, J. Cheminf. 3 (2011) 2.

171. 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 Comp. 8 (2012) 75-79.

172. 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. T. H. Khan, I. Sylte, 
N. Kurita, J. Mol. Graph. Mod. 33 (2012) 1-11

173. 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.

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

175. 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.

176. 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.

177. 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.

178. 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.

179. 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.

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

181. The fragment molecular orbital and systematic molecular fragmentation
methods applied to water clusters. S. R. Pruitt, M. A. Addicoat, M. A. Collins,
M. S. Gordon, Phys. Chem. Chem. Phys. 14 (2012) 7752-7764.

182. Analytic gradient for second order Moeller-Plesset perturbation theory
with the polarizable continuum model based on the fragment molecular orbital
method. T. Nagata, D. G. Fedorov, H. Li, K. Kitaura, J. Chem. Phys. 136 (2012)
204112.

183. Geometry optimizations of open-shell systems with the fragment
molecular orbital method. S. R. Pruitt, D. G. Fedorov, M. S. Gordon, J. Phys. 
Chem. A 116 (2012) 4965-4974.

184. Origin of the inhibitory activity of 4-O-substituted sialic derivatives
of human parainfluenza virus. Y. Itoh, A. Sando, K. Ikeda, T. Suzuki, H. Tokiwa,
Glycoconj. J. 29 (2012) 231-237.

185. FMO-MD Simulations on the hydration of formaldehyde in water solution
with constraint dynamics. M. Sato, H. Yamataka, Y. Komeiji, Y. Mochizuki,
Chem. Eur. J. 18 (2012) 9714-9721.

186. Intrinsic edge asymmetry in narrow zigzag hexagonal heteroatomic
nanoribbons causes their subtle uniform curvature. P. V. Avramov, D. G. 
Fedorov, P. B. Sorokin, S. Sakai, S. Entani, M. Ohtomo, Y. Matsumoto, H. 
Naramoto, J. Phys. Chem. Lett. 3 (2012) 2003-2008.

187. Unrestricted Hartree-Fock based on the fragment molecular orbital method: 
energy and its analytic gradient. H. Nakata, D. G. Fedorov, T. Nagata, S.
Yokojima, K. Ogata, K. Kitaura, S. Nakamura, J. Chem. Phys. 137 (2012) 044110.

188. Reducing the scaling of the fragment molecular orbital method using the
multipole method. C. H. Choi, D. G. Fedorov, Chem. Phys. Lett. 543 (2012)
159-165. 

189. Analytic gradient for the embedding potential with approximations in the
fragment molecular orbital method. T. Nagata, D. G. Fedorov, K. Kitaura,
Chem. Phys. Lett. 544 (2012) 87-93.

190. Analysis of solute-solvent interactions in the fragment molecular orbital
method interfaced with effective fragment potentials: theory and application
to a solvated griffithsin-carbohydrate complex. T. Nagata, D. G. Fedorov, 
T. Sawada, K. Kitaura, J. Phys. Chem. A 116 (2012) 9088-9099.

191. Ab initio molecular simulations on specific interactions between
amyloid beta and monosaccharides. K. Nomura, A. Okamoto, A. Yano, S. Higai, 
T. Kondo, S. Kamba, N. Kurita, Chem. Phys. Lett. 547 (2012) 89-96.

192. Fragment molecular orbital study on electron tunneling mechanisms in
bacterial photosynthetic reaction center. H. Kitoh-Nishioka, K. Ando,
J. Phys. Chem. B 116 (2012) 12933-12945.

193. The fragment molecular orbital method and understanding monomer
polarization. C. D. M. Churchill, Chem. Phys. Lett. 554 (2012) 185-189.

194. Heuristic static load-balancing algorithm applied to the fragment
molecular orbital method. Y. Alexeev, A. Mahajan, S. Leyffer, G. Fletcher, 
D. G. Fedorov Proc. Supercomputing 2012, IEEE Computer Society, Salt Lake 
City, 2012.

195. Ab Initio Path Integral Molecular Dynamics and Monte Carlo Simulations
for Water Trimer and Oligopeptide. T. Fujita, M.-A. Kusa, T. Fujiwara, 
Y. Mochizuki, S. Tanaka, In Advances in Quantum Monte Carlo, Ch. 15, 2012, 
ACS Symposium Series, Vol. 1094, pp. 187-199.

196. Recent advances in fragment molecular orbital-based molecular
dynamics (FMO-MD) simulations, Y. Komeiji, Y. Mochizuki, T. Nakano, H. Mori,
In Molecular Dynamics - Theoretical Developments and Applications in
Nanotechnology and Energy, L. Wang (Ed.), Intech, 2012, pp. 3-24.

197. Fragment molecular orbital molecular dynamics with the fully analytic
energy gradient. K. R. Brorsen, N. Minezawa, F. Xu, T. L. Windus, M. S.
Gordon, J. Chem. Theory Comp. 8 (2012) 5008-5012.

198. GAMESS as a free quantum-mechanical platform for drug research.
Y. Alexeev, M. P. Mazanetz, O. Ichihara, D. G. Fedorov, Curr. Top. Med. Chem.
12 (2012) 2013-2033.

199. Towards quantum-based modeling of enzymatic reaction pathways:
application to the acetylholinesterase catalysis. I. V. Polyakov, B. L. 
Grigorenko, A. A. Moskovsky, V. M. Pentkovski, A. V. Nemukhin, Chem. Phys. 
Lett. 556 (2013) 251-255.

200. Statistical correction to effective interactions in the fragment
molecular orbital method. S. Tanaka, C. Watanabe, Y. Okiyama, Chem. Phys. 
Lett. 556 (2013) 272-277.

201. A theoretical study of the two binding modes between lysozyme and tri-NAG 
with an explicit solvent model based on the fragment molecular orbital method.
T. Ishikawa, R. R. Burri, Y. O. Kamatari, S. Sakuraba, N. Matubayasi, 
A. Kitao, K. Kuwata, Phys. Chem. Chem. Phys. 15 (2013) 3646-3654.

202. Open-shell pair interaction energy decomposition analysis (PIEDA):
Formulation and application to the hydrogen abstraction in tripeptides.
M. C. Green, D. G. Fedorov, K. Kitaura, J. S. Francisco, L. V. Slipchenko,
J. Chem. Phys. 138 (2013) 074111.

203. A minimal implementation of the AMBER-PAICS interface for ab initio
FMO-QM/MM-MD simulation. T. Okamoto, T. Ishikawa, Y. Koyano, N. Yamamoto,
K. Kuwata, M. Nagaoka, Bull. Chem. Soc. Jap. 86 (2013) 210-222. 

204. Comparison of the local structural stabilities of mammalian prion protein
(PrP) by fragment molecular orbital calculations. K. Hasegawa, S. Mohri, 
T. Yokoyama, Prion. 7 (2013) 185-191.

205. Three- and four-body corrected fragment molecular orbital calculations
with a novel subdividing fragmentation method applicable to structure-based
drug design. C. Watanabe, K. Fukuzawa, Y. Okiyama, T. Tsukamoto, A. Kato, 
S. Tanaka, Y. Mochizuki, T. Nakano, J. Mol. Graph. Modell. 41 (2013) 31-42.

206. Modeling of peptide-silica interaction based on four-body corrected
fragment molecular orbital (FMO4) calculations. Y. Okiyama, T. Tsukamoto, 
C. Watanabe, K. Fukuzawa, S. Tanaka, Y. Mochizuki, Chem. Phys. Lett. 566 
(2013) 25-31.

207. Protein-specific force field derived from the fragment molecular orbital
method can improve protein-ligand binding interactions. L. Chang, T. Ishikawa, 
K. Kuwata, S. Takada, J. Comp. Chem. 34 (2013) 1251-1257.

208. Analytic second derivatives of the energy in the fragment molecular
orbital method. H. Nakata, T. Nagata, D. G. Fedorov, S. Yokojima, K. Kitaura, 
S. Nakamura, J. Chem. Phys. 138 (2013) 164103.

209. Stable conformation of full-length amyloid-beta (1-42) monomer in water:
replica exchange molecular dynamics and ab initio molecular orbital
simulations. A. Okamoto, A. Yano, K. Nomura, S. Higai, N. Kurita,
Chem. Phys. Lett. 577 (2013) 131-137.

210. Diffusion energy profiles in silica mesoporous molecular sieves modelled
with the fragment molecular orbital method. L. Roskop, D. G. Fedorov,
M. S. Gordon, Mol. Phys. 111 (2013) 1622-1629.

211. The effects of vitronectin on specific interactions between 
urokinase-type plasminogen activator and its receptor: ab initio molecular 
orbital calculations. T. Kasumi, K. Araki, T. Ohyama, S. Tsuji, E. Yoshikawa, 
H. Kobayashi, N. Kurita, Mol. Sim. 39 (2013) 769-779.

212. Trimer effects in fragment molecular orbital-linear combination of
molecular orbitals calculation of one-electron orbitals for biomolecules.
T. Kobori, K. Sodeyama, T. Otsuka, Y. Tateyama, S. Tsuneyuki,
J. Chem. Phys. 139 (2013) 094113.

213. Multi-state approach to chemical reactivity in fragment based quantum
chemistry calculations. A. W. Lange, G. A. Voth, J. Chem. Theory Comp. 
9 (2013) 4018-4025.

214. Ab Initio Study of Molecular Interactions in Cellulose Ialpha. 
A. Devarajan, S. Markutsya, M. H. Lamm, X. Cheng, J. C. Smith, J. Y. Baluyut,
Y. Kholod, M. S. Gordon, T. L. Windus, J. Phys. Chem. B 117 (2013) 10430-10443.

215. Crystal structure of a complex of human chymase with its benzimidazole 
derived inhibitor. Y. Matsumoto, S. Kakuda, M. Koizumi, T. Mizuno, Y. Muroga, 
T. Kawamura, M. Takimoto-Kamimura, J. Synchr. Rad. 20 (2013) 914-918.

216. Chemical description of the interaction between glycan ligand and
Siglec-7 using ab initio FMO method and classical MD simulation.
A. Ueno-Noto, S. Ise, K. Takano, J. Theor. Comp. Chem. 12 (2013) 1350060.

217. Octahedral point-charge model and its application to fragment molecular 
orbital calculations of chemical shifts. Q. Gao, S. Yokojima, D. G. Fedorov,
K. Kitaura, M. Sakurai, S. Nakamura, Chem. Phys. Lett. 593 (2014) 165-173.

218. Accuracy of the fragment molecular orbital (FMO) calculations for DNA:
Total energy, molecular orbital, and inter-fragment interaction energy.
K. Fukuzawa, C. Watanabe, I. Kurisaki, N. Taguchi, Y. Mochizuki, T. Nakano, 
S. Tanaka, Y. Komeiji, Comp. Theor. Chem. 1034 (2014) 7-16.

219. Difference in dimer conformation between amyloid-beta(1-42) and
(1-3) proteins: Replica exchange molecular dynamics simulations in water.
A. Yano, A. Okamoto, K. Nomura, S, Higai, N. Kurita,
Chem. Phys. Lett. 595-596 (2014) 242-249.

220. Affinity of HIV-1 antibody 2G12 with monosaccharides: A theoretical study
based on explicit and implicit water models. Y. Koyama, K. Ueno-Noto, K. Takano,
Comp. Biol. Chem. 49 (2014) 36-44.

221. Use of an auxiliary basis set to describe the polarization in the
fragment molecular orbital method. D. G. Fedorov, K. Kitaura,
Chem. Phys. Lett. 597 (2014) 99-105.

222. Molecular interactions of the quinone electron acceptors QA, QB, and QC
in photosystem II as studied by the fragment molecular orbital method.  
K. Hasegawa, T. Noguchi, Photosynth. Res. 120 (2014) 113-123.

223. Derivatives of the approximated electrostatic potentials in unrestricted
Hartree-Fock based on the fragment molecular orbital method and an
application to polymer radicals. H. Nakata, D. G. Fedorov, S. Yokojima,
K. Kitaura, S. Nakamura, Theor. Chem. Acc. 133 (2014) 1477.

224. Unrestricted density functional theory based on the fragment
molecular orbital method for the ground and excited state calculations of 
large systems. H. Nakata, D. G. Fedorov, S. Yokojima, K. Kitaura, M. Sakurai, 
S. Nakamura, J. Chem. Phys. 140 (2014) 144101.

225. Effect of D23N mutation on the dimer conformation of amyloid beta-proteins:
Ab initio molecular simulations in water. A. Okamoto, A. Yano, K. Nomura, 
S. Higai, N. Kurita, J. Mol. Graph. Model. 50 (2014) 113-124.

226. Electron-correlated fragment-molecular-orbital calculations for 
biomolecular and nano systems. S. Tanaka, Y. Mochizuki, Y. Komeiji, Y. Okiyama,
K. Fukuzawa, Phys. Chem. Chem. Phys. 16 (2014) 10310-10344.

227. Efficient vibrational analysis for unrestricted Hartree-Fock based on the
fragment molecular orbital method. H. Nakata, D. G. Fedorov, S. Yokojima, 
K. Kitaura, S. Nakamura, Chem. Phys. Lett. 603 (2014) 67-74.

228. Charge clamps of lysines and hydrogen bonds play key roles in the 
mechanism to fix helix 12 in the agonist and antagonist positions of estrogen 
receptor alpha: intramolecular interactions studied by the ab initio fragment 
molecular orbital method. C. Watanabe, K. Fukuzawa, S. Tanaka, S. Aida-Hyugaji,
J. Phys. Chem. B 118 (2014) 4993-5008.

229. Efficient implementation of the three-dimensional reference interaction 
site model method in the fragment molecular orbital method. N. Yoshida, 
J. Chem. Phys. 140 (2014) 214118.

230. Interaction energy analysis on specific binding of influenza virus
hemagglutinin to avian and human sialosaccharide receptors: Importance of
mutation-induced structural change. S. Anzaki, C. Watanabe, K. Fukuzawa, 
Y. Mochizuki, S. Tanaka, J. Mol. Graph. Model. 53 (2014) 48-58.

231. Effective ion mobility calculations for macromolecules by scattering on
electron clouds. Y. Alexeev, D. G. Fedorov, A. A. Shvartsburg,
J. Phys. Chem. A 118 (2014) 6763-6772.

232. Simulations of Raman spectra using the fragment molecular orbital method.
H. Nakata, D. G. Fedorov, S. Yokojima, K. Kitaura, S. Nakamura,
J. Chem. Theory Comput. 10 (2014) 3689-3698.

233. In silico prediction of mutant HIV-1 proteases cleaving a target sequence. 
J. H. Jensen, M. Willemoes, J. R. Winther, L. De Vico, PLoS ONE 9 (2014) e95833.

234. The use of many-body expansions and geometry optimizations in
fragment-based methods. D. G. Fedorov, N. Asada, I. Nakanishi, K. Kitaura,
Acc. Chem. Res. 47 (2014) 2846-2856.

235. Efficient molecular dynamics simulations of multiple radical center
systems based on the fragment molecular orbital method. H. Nakata,
M. W. Schmidt, D. G. Fedorov, K. Kitaura, S. Nakamura, M. S. Gordon,
J. Phys. Chem. A 118 (2014) 9762-9771.

236. Theoretical study on the hydration structure of divalent radium ion using
fragment molecular orbital - molecular dynamics (FMO-MD) simulation.
A. Matsuda, H. Mori, J. Sol. Chem. 43 (2014) 1669-1675.

237. Ab initio molecular simulations for proposing potent inhibitors to
butyrylcholinesterases. T. Murakawa, Y. Matsushita, T. Suzuki, M. T. H. Khan,
N. Kurita, J. Mol. Graph. Modell. 54 (2014) 54-61.

238. Density-functional tight-binding combined with the fragment molecular
orbital method. Y. Nishimoto, D. G. Fedorov, S. Irle, J. Chem. Theory Comput.
10 (2014) 4801-4812.

239. Novel approach for identifying key residues in enzymatic reactions:
proton abstraction in ketosteroid isomerase. M. Ito, T. Brinck, J. Phys. Chem.
B 118 (2014) 13050-13058.

240. Analytic gradient for density functional theory based on the fragment
molecular orbital method. K. R. Brorsen, F. Zahariev, H. Nakata, D. G.
Fedorov, M. S. Gordon, J. Chem. Theory Comput. 10 (2014) 5297-5307.

241. Explicit solvation modulates intra- and inter-molecular interactions within
DNA: Electronic aspects revealed by the ab initio fragment molecular orbital
(FMO) method. K. Fukuzawa, I. Kurisaki, C. Watanabe, Y. Okiyama, Y. Mochizuki, 
S. Tanaka, Y. Komeiji, Comp. Theor. Chem. 1054 (2015) 29-37.

242. Charge-transfer matrix elements by FMO-LCMO approach: Hole transfer in DNA
with parameter tuned range-separated DFT. H. Kitoh-Nishioka, K. Ando,
Chem. Phys. Lett. 621 (2015) 96-101.

243. Quality assessment of predicted protein models using energies calculated
by the fragment molecular orbital method. D. Simoncini, H. Nakata, K. Ogata, 
S. Nakamura, K. Y. J. Zhang, Mol. Inf. 34 (2015) 97-104.

244. Thermodynamics of binding of di- and tetrasubstituted naphthalene diimide
ligands to DNA G-quadruplex. G. Prato, S. Silvent, S. Saka, M. Lamberto, 
D. Kosenkov, J. Phys. Chem. B 119 (2015) 3335-3347.

245. Analytic second derivative of the energy for density functional theory
based on the three-body fragment molecular orbital method. H. Nakata, 
D. G. Fedorov, F. Zahariev, M. W. Schmidt, K. Kitaura, M. S. Gordon,
S. Nakamura, J. Chem. Phys. 142 (2015) 124101.

246. Hydration effects on enzyme-substrate complex of nylon oligomer
hydrolase: inter-fragment interaction energy study by the fragment molecular 
orbital method. H. Ando, Y. Shigeta, T. Baba, C. Watanabe, Y. Okiyama, 
Y. Mochizuki, M. Nakano, Mol. Phys. 113 (2015) 319-326.

247. Massively parallel electron correlation calculations for large systems.
A. D. Findlater, F. Zahariev, M. S. Gordon, J. Phys. Chem. A 119 (2015) 
3587-3593.

248. Binding affinity between AhR and exogenous/endogenous ligands: molecular 
simulations and biological experiment. S. Miyagi, K. Murata, K. Sashino, 
S. Sawamura, S. Uruno, S. Yoshimura, E. Akahoshi, M. Ishihara-Sugano, S. Itoh, 
N. Kurita, Mol. Sim. 41 (2015) 555-563.

249. Modeling of hydroxyapatite-peptide interaction based on fragment m
molecular orbital method. K. Kato, K. Fukuzawa, Y. Mochizuki,
Chem. Phys. Lett. 629 (2015) 58-64.

250. Novel type of virtual ligand screening on the basis of quantum-chemical 
calculations for protein-ligand complexes and extended clustering techniques.
R. Kurauchi, C. Watanabe, K. Fukuzawa, S. Tanaka, Comp. Theor. Chem. 1061
(2015) 12-22.

251. Pharmacophore modeling for anti-chagas drug design using the fragment
molecular orbital method. R. Yoshino, N. Yasuo, D. K. Inaoka, Y. Hagiwara, 
K. Ohno, M. Orita, M. Inoue, T. Shiba, S. Harada, T. Honma, E. O. Balogun, 
J. R. Rocha, C. A. Montanari, K. Kita, M. Sekijima, PLoS ONE 10 (2015) e0125829.

252. Extension of the fragment molecular orbital method to treat large
open-shell systems in solution. H. Nakata, D. G. Fedorov, K. Kitaura,
S. Nakamura, Chem. Phys. Lett. 635 (2015) 86-92.

253. Simulations of chemical reactions with the frozen domain formulation of
the fragment molecular orbital method. H. Nakata, D. G. Fedorov, T. Nagata, 
K. Kitaura, S. Nakamura, J. Chem. Theory Comput. 11 (2015) 3053-3064.

254. Third-order density-functional tight-binding combined with the fragment
molecular orbital method. Y. Nishimoto, D. G. Fedorov, S. Irle,
Chem. Phys. Lett. 636 (2015) 90-96.

255. Assessment and acceleration of binding energy calculations for 
protein-ligand complexes by the fragment molecular orbital method.
T. Otsuka, N. Okimoto, M. Taiji, J. Comput. Chem. 36 (2015) 2209-2218.

256. Large-scale quantum-mechanical molecular dynamics simulations using 
density-functional tight-binding combined with the fragment molecular orbital 
method. Y. Nishimoto, H. Nakata, D. G. Fedorov, S. Irle, J. Phys. Chem. Lett. 
6 (2015) 5034-5039.

257. Electron transfer pathway analysis in bacterial photosynthetic reaction 
center. H. Kitoh-Nishioka, K. Ando, in "Chemical Science of pi-Electron 
Systems", T. Akasaka, A. Osuka, S. Fukuzumi, H. Kandori, Y. Aso (Eds), 
Springer, Tokyo, pp 657-673, 2015.

258. Change in specific interactions between lactose repressor protein and DNA 
induced by ligand binding: molecular dynamics and molecular orbital 
calculations. Y. Matsushita, T. Murakawa, K. Shimamura, T. Ohyama, M. Oishi, 
N. Kurita, Mol. Sim. 42 (2016) 242-256.

259. The fragment molecular orbital method reveals new insight into the 
chemical nature of GPCR-ligand interactions. A. Heifetz, E. I. Chudyk, 
L. Gleave, M. Aldeghi, V. Cherezov, D. G. Fedorov, P. C. Biggin, M. J. Bodkin,
J. Chem. Inf. Model. 56 (2016) 159-172.

260. Radical damage in lipids investigated with the fragment molecular orbital 
method. M. C. Green, H. Nakata, D. G. Fedorov, L. V. Slipchenko,
Chem. Phys. Lett. 651 (2016) 56-61.

261. Using the fragment molecular orbital method to investigate 
agonist-orexin-2 receptor interactions. A. Heifetz, M. Aldeghi, E. I. Chudyk, 
D. G. Fedorov, M. J. Bodkin, P. C. Biggin, Biochem. Soc. Trans. 44 (2016) 
574-581.

262. Importance of three-body interactions in molecular dynamics simulations 
of water demonstrated with the fragment molecular orbital method. S. R. Pruitt, 
H. Nakata, T. Nagata, M. Mayes, Y. Alexeev, G. Fletcher, D. G. Fedorov, 
K. Kitaura, M. S. Gordon, J. Chem. Theory Comput. 12 (2016) 1423-1435.

263. Interaction analysis of FABP4 inhibitors by X-ray crystallography and 
fragment molecular orbital analysis. U. Tagami, K. Takahashi, S. Igarashi, 
C. Ejima, T. Yoshida, S. Takeshita, W. Miyanaga, M. Sugiki, M. Tokumasu, 
T. Hatanaka, T. Kashiwagi, K. Ishikawa, H. Miyano, T. Mizukoshi,
ACS Med. Chem. Lett. 7 (2016) 435-439.

264. Subsystem analysis for the fragment molecular orbital method and its 
application to protein-ligand binding in solution. D. G. Fedorov, K. Kitaura,
J. Phys. Chem. A 120 (2016) 2218-2231.

265. Fragment molecular orbital method applied to lead optimization of novel 
interleukin-2 inducible T-cell kinase (ITK) inhibitors. A. Heifetz, G. Trani, 
M. Aldeghi, C. H. MacKinnon, P. A. McEwan, F. A. Brookfield, E. I. Chudyk,
M. Bodkin, Z. Pei, J. D. Burch, D. F. Ortwine, J. Med. Chem. 59 (2016) 
4352-4363.

266. Applications of the fragment molecular orbital method to drug research.
M. P. Mazanetz, E. Chudyk, D. G. Fedorov,  Y. Alexeev, In Computer aided drug 
discovery.  W. Zhang, Ed., Springer, New York, 2016, pp. 217-255.

267. Fragment molecular orbital study of the cAMP-dependent protein kinase 
catalyzed phosphoryl transfer: a comparison with the differential transition 
state stabilization method. H. Öbe , T. Brinck,
Phys. Chem. Chem. Phys. 18 (2016) 15153-15161.

268. Analytic second derivative of the energy for density-functional
tight-binding combined with the fragment molecular orbital method.
H. Nakata, Y. Nishimoto, D. G. Fedorov, J. Chem. Phys. 145 (2016) 044113.

269. The fragment molecular orbital method combined with density-functional
tight-binding and the polarizable continuum model. Y. Nishimoto, D. G. Fedorov,
Phys. Chem. Chem. Phys. 18 (2016) 22047-22061.

270. Water molecules inside protein structure affect binding of monosaccharides
with HIV-1 antibody 2G12. K. Ueno-Noto, K. Takano, J. Comput. Chem. 37 (2016) 
2341-2348.

271.  Hydration of ligands of influenza virus neuraminidase studied by the 
fragment molecular orbital method. K. Tokuda, C. Watanabe, Y. Okiyama, 
Y. Mochizuki, K. Fukuzawa, Y. Komeiji, J. Mol. Graph. Model. 69 (2016) 144-153.

272. Fragment molecular orbital nonadiabatic molecular dynamics for condensed 
phase systems. B. Nebgen, O. V. Prezhdo, J. Phys. Chem. A 120 (2016) 7205-7212.

273. FMO3-LCMO study of electron transfer coupling matrix element and pathway:
Application to hole transfer between two tryptophans through cis- and 
trans-polyproline-linker systems. H. Kitoh-Nishioka, K. Ando, J. Chem. Phys. 
145 (2016) 114103.

274. Comparative binding analysis of dipeptidyl peptidase IV (DPP-4) with
antidiabetic drugs - An ab initio fragment molecular orbital study. 
S. Arulmozhiraja, N. Matsuo, E. Ishitsubo, S. Okazaki, H. Shimano, H. Tokiwa, 
PLoS ONE 11 (2016) e0166275.

275. Efficient geometry optimization of large molecular systems in solution 
using the fragment molecular orbital method. H. Nakata, D. G. Fedorov, 
J. Phys. Chem. A 120 (2016) 9794-9804.

276. Fragment molecular orbital (FMO) calculations on DNA by a scaled 
third-order Moller-Plesset perturbation (MP2.5) scheme. H. Yamada, 
Y. Mochizuki, K. Fukuzawa, Y. Okiyama, Y. Komeiji, Comp. Theor. Chem. 1101
(2017) 46-54.

277. Semi-empirical quantum evaluation of peptide - MHC class II binding.
R. González, C. F. Suárez, H. J. Bohórquez, M. A. Patarroyo, M. E. Patarroyo,
Chem. Phys. Lett. 668 (2017) 29-34.

278. Three-body expansion of the fragment molecular orbital method combined 
with density-functional tight-binding. Y. Nishimoto, D. G. Fedorov,
J. Comp. Chem. 38 (2017) 406-418.

279. Mapping interaction energies in chorismate mutase with the fragment 
molecular orbital method. S. R. Pruitt, C. Steinmann, J. Phys. Chem. A 121 
(2017) 1797-1807.

280. Specific interactions between amyloid-beta peptides in an amyloid-beta 
hexamer with three-fold symmetry: Ab initio fragment molecular orbital 
calculations in water. H. Ishimura, S. Tomioka, R. Kadoya, K. Shimamura, 
A. Okamoto, S. Shulga, N. Kurita, Chem. Phys. Lett. 672 (2017) 13-20.

281. Application of the fragment molecular orbital method analysis to 
fragment-based drug discovery of BET (bromodomain and extra-terminal proteins)
inhibitors. M. Ozawa, T. Ozawa, K. Ueda, J. Mol. Graph. Model. 74 (2017) 73-82.

282. Rapid and accurate assessment of GPCR-ligand interactions using the 
fragment molecular orbital-based density-functional tight-binding method
I. Morao, D. G. Fedorov, R. Robinson, M. Southey, A. Townsend-Nicholson, 
M. J. Bodkin, A. Heifetz, J. Comp. Chem. 38 (2017) 1987-1990.

283. Multiscale simulations on charge transport in covalent organic frameworks 
including dynamics of transfer integrals from the FMO-DFTB/LCMO approach.
H. Kitoh-Nishioka, K. Welke, Y. Nishimoto, D. G. Fedorov, Stephan Irle,
J. Phys. Chem. C 121 (2017) 17712-17726.

284. Specific interactions between androgen receptor and its ligand: ab initio 
molecular orbital calculations in water. I. Kobayashi, R. Takeda, R. Suzuki, 
K. Shimamura, H. Ishimura, R. Kadoya, K. Kawai, M. Takimoto-Kamimura, 
N. Kurita, J. Mol. Graph. Model. 75 (2017) 383-389.

285. Specific interactions between vitamin-D receptor and its ligands: 
Ab initio molecular orbital calculations in water. R. Takeda, I. Kobayashi, 
K. Shimamura, H. Ishimura, R. Kadoya, K. Kawai, A. Kittaka, 
M. Takimoto-Kamimura, N. Kurita, J. Ster. Biochem. Mol. Biol. 171 (2017) 75-79.

286. Dissipative particle dynamics (DPD) simulations with fragment molecular 
orbital (FMO) based effective parameters for 1-Palmitoyl-2-oleoyl phosphatidyl 
choline (POPC) membrane. H. Doi, K. Okuwaki, Y. Mochizuki, T. Ozawa, 
K. Yasuoka, Chem. Phys. Lett. 684 (2017) 427-432.

287. Relating stacking structures and charge transport in crystal polymorphs of
the pyrrole-based pi-conjugated molecule. T. Fujita, Y. Haketa, H. Maeda, 
T. Yamamoto, Org. Electr. 49 (2017) 53-63.

288. Specific interactions between zinc metalloproteinase and its inhibitors: 
Ab initio fragment molecular orbital calculations. A. Ara, R. Kadoya, 
H. Ishimura, K. Shimamura, I. Sylte, N. Kurita, J. Mol. Graph. Model. 75 (2017)
277-286.

289. Proposal for novel curcumin derivatives as potent inhibitors against 
Alzheimer's disease: Ab initio molecular simulations on the specific 
interactions between amyloid-beta peptide and curcumin. S. Ota, M. Fujimori, 
H. Ishimura, S. Shulga, N. Kurita, Chem. Phys. Lett. 685 (2017) 482-489.

290. The role of CH/pi interactions in the high affinity binding of 
streptavidin and biotin. M. Ozawa, T. Ozawa, M. Nishio, K. Ueda,
J. Mol. Graph. Model. 75 (2017) 117-124.

291. The FMO analysis of the molecular interaction of fentanyl derivatives with
the mu-opioid receptor. M. Jaronczyk, P. F. J. Lipinski, J. Cz. Dobrowolski,
J. Sadlej, Chem. Pap. 71 (2017) 1429-1443.

292. Theoretical analyses of triplet-triplet annihilation process of 
9,10-diphenylanthracene in solution. R. Sato, H. Kitoh-Nishioka, T. Yanai, 
Y. Shigeta, Chem. Lett. 46 (2017) 873-875.

293. Many-body expansion of the Fock matrix in the fragment molecular orbital 
method. D. G. Fedorov, K. Kitaura, J. Chem. Phys. 147 (2017) 104106.

294. The fragment molecular orbital method: theoretical development, 
implementation in GAMESS, and applications. D. G. Fedorov, WIREs: 
Comp. Mol. Sc. 7 (2017) e1322.

295. Modeling and visualization for the fragment molecular orbital method with 
the graphical user interface FU, and analyses of protein-ligand binding.
D. G. Fedorov, K. Kitaura, in Fragmentation: toward Accurate calculations on 
complex molecular systems. M. S. Gordon, Ed. Wiley, Hoboken, 2017, pp. 119-139.

296. Novel genes and mutations in patients affected by recurrent pregnancy loss.
P. Quintero-Ronderos, E. Mercier, M. Fukuda, R. Gonzalez, C. F. Suarez,
M. A. Patarroyo, D. Vaiman, J.-C. Gris, P. Laissue, PLoS ONE 12 (2017) e0186149.

297. 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.
C. Watanabe, H. Watanabe, K. Fukuzawa, L. J. Parker, Y. Okiyama, H. Yuki, 
S. Yokoyama, H. Nakano, S. Tanaka, T. Honma, J. Chem. Inf. Model. 2017, 57, 
2996-3010.

298. Exploring GPCR-ligand interactions with the fragment molecular orbital 
(FMO) Method. E. I. Chudyk, L. Sarrat, M. Aldeghi, D. G. Fedorov, M. J. Bodkin,
T. James, M. Southey, R. Robinson, I. Morao, A. Heifetz, in Computational 
Methods for GPCR Drug Discovery. A. Heifetz (Ed.), Humana Press, New York, 
2018, pp. 179-195.

299. Fluorescent pseudorotaxanes of a quinodicarbocyanine dye with gamma 
cyclodextrin. O. M. Bernstein, T. E. McGee, L. E. Silzel, J. W. Silzel,
Spectr. Acta A: Mol. Biomol. Spectr. 189 (2018) 202-214.

300. Fragment molecular orbital based parametrization procedure for mesoscopic 
structure prediction of polymeric materials. K. Okuwaki, Y. Mochizuki, H. Doi, 
T. Ozawa, J. Phys. Chem. B 122 (2018) 338-347.

301. Specific interactions between mycobacterial FtsZ protein and curcumin 
derivatives: Molecular docking and ab initio molecular simulations.
M. Fujimori, H. Sogawa, S. Ota, P. Karpov, S. Shulga, Y. Blume, N. Kurita,
Chem. Phys. Lett. 692 (2018) 166-173.

302. Pair interaction energy decomposition analysis for density functional
theory and density-functional tight-binding with an evaluation of energy
fluctuations in molecular dynamics. D. G. Fedorov, K. Kitaura,
J. Phys. Chem. A 122 (2018) 1781-1795

303. Adaptive frozen orbital treatment for the fragment molecular orbital
method combined with density-functional tight-binding. Y. Nishimoto,
D. G. Fedorov, J. Chem. Phys. 148 (2018) 064115.

304. Ab initio quantum chemical calculation of electron density, electrostatic
potential, and electric field of biomolecule based on fragment molecular 
orbital method. T. Ishikawa, Int. J. Quantum Chem. 118 (2018) e25535.

305. Development of the fragment molecular orbital method for calculating 
nonlocal excitations in large molecular systems. T. Fujita, Y. Mochizuki,
J. Phys. Chem. A 122 (2018) 3886-3898.

306. Proposal of potent inhibitors for vitamin-D receptor based on ab initio 
fragment molecular orbital calculations. R. Takeda, I. Kobayashi, R. Suzuki, 
K. Kawai, A. Kittaka, M. Takimoto-Kamimura, N. Kurita, J. Mol. Graph. Model. 
80 (2018) 320-326.

307. Application of singular value decomposition to the inter-fragment 
interaction energy analysis for ligand screening. K. Maruyama, Y. Sheng, 
H. Watanabe, K. Fukuzawa, S. Tanaka, Comp. Theor. Chem. 1132 (2018) 23-34.

308. Molecular association model of PPARalpha and its new specific and 
efficient ligand, pemafibrate: Structural basis for SPPARMalpha. Y. Yamamoto, 
K. Takei, S. Arulmozhiraja, V. Sladek, N. Matsuo, S. Han, T. Matsuzaka, 
M. Sekiya, T. Tokiwa, M. Shoji, Y. Shigeta, Y. Nakagawa, H. Tokiwa, H. Shimano,
Biochem. Biophys. Res. Comm. 499 (2018) 239-245.

309. Towards first-principles calculation of electronic excitations in the ring
of the protein-bound bacteriochlorophylls. I. V. Polyakov, M. G. Khrenova, 
A. A. Moskovsky, B. M. Shabanov, A. V. Nemukhin, Chem. Phys. 505 (2018) 34-39.

310. Use of the multilayer fragment molecular orbital method to predict the 
rank order of protein-ligand binding affinities: A Case study using tankyrase 2
inhibitors. N. Okimoto, T. Otsuka, Y. Hirano, M. Taiji, ACS Omega 3 (2018)
4475-4485.

311. Analysis of solute-solvent interactions using the solvation model density 
combined with the fragment molecular orbital method. D. G. Fedorov,
Chem. Phys. Lett. 702 (2018) 111-116.

312. Empirical corrections and pair interaction energies in the fragment 
molecular orbital method. D. G. Fedorov, J. C. Kromann, J. H. Jensen,
Chem. Phys. Lett. 706 (2018) 328-333.

313. Computational analysis of the interaction energies between amino acid 
residues of the measles virus hemagglutinin and its receptors. F. Xu, S. 
Tanaka, Y. Shimane, M. Iwasawa, K. Ohishi, T. Maruyama, Viruses 10 (2018) 236.

314. Characterization of crystal water molecules in a high-affinity inhibitor 
and hematopoietic prostaglandin D synthase complex by interaction energy
studies. D. Takaya, K. Inaka, A. Omura, K. Takenuki, M. Kawanishi, Y. Yabuki,
Y. Nakagawa, K. Tsuganezawa, N. Ogawa, C. Watanabe, T. Honma, K. Aritake,
Y. Urade, M. Shirouzu, A. Tanaka, Bioorg. Med. Chem. 26 (2018) 4726-4734.

315. Application of the fragment molecular orbital method to discover novel 
natural products for prion disease. J. Choi, H. Kim, X. Jin, H. Lim, S. Kim,
I. Roh, H. Kang, K. Tai No, H. Sohn, Sc. Rep. 8 (2018) 13063.

316. Fragment molecular orbital study of the interaction between sarco/
endoplasmic reticulum Ca(2+)-ATPase and its inhibitor thapsigargin toward 
anti-malarial development. T. Ishikawa, S. Mizuta, O. Kaneko, K. Yahata,
J. Phys. Chem. B 122 (2018) 7970-7977.

317. Fragment molecular orbital calculations with implicit solvent based 
on the Poisson-Boltzmann equation: implementation and DNA study.
Y. Okiyama, T. Nakano, C. Watanabe, K. Fukuzawa, Y. Mochizuki, S. Tanaka,
J. Phys. Chem. B 122 (2018) 4457-4471.

318. Electron transfer pathways of cyclobutane pyrimidine dimer photolyase 
revisited. R. Sato, H. Kitoh-Nishioka, K. Ando, T. Yamato,
J. Phys. Chem. B 122 (2018) 6912-6921.

319. Characterization of crystal water molecules in a high-affinity inhibitor 
and hematopoietic prostaglandin D synthase complex by interaction energy
studies. D. Takaya, K. Inaka, A. Omura, K. Takenuki, M. Kawanishi, Y. Yabuki, 
Y. Nakagawa, K. Tsuganezawa, N. Ogawa, C. Watanabe, T. Honma, K. Aritake, 
Y. Urade, M. Shirouzu, A. Tanaka, Bioorg. Med. Chem. 26 (2018) 4726-4734.

320. RI-MP3 calculations of biomolecules based on the fragment molecular 
orbital method. T. Ishikawa, K. Sakakura, Y. Mochizuki, J. Comp. Chem. 39
(2018) 1970-1978.

321. Theoretical analyses on water cluster structures in polymer electrolyte 
membrane by using dissipative particle dynamics simulations with fragment 
molecular orbital based effective parameters. K. Okuwaki, Y. Mochizuki, 
H. Doi, S. Kawada, T. Ozawa, K. Yasuoka, RSC Adv. 8 (2018) 34582-34595.

322. Analytic second derivatives for the efficient electrostatic embedding in 
the fragment molecular orbital method. H. Nakata, D. G. Fedorov, J. Comp. Chem.
39 (2018) 2039-2050.

323. Interaction between a single-stranded DNA and a binding protein viewed 
by the fragment molecular orbital method. Y. Komeiji, Y. Okiyama, Y. Mochizuki,
K. Fukuzawa, Bull. Chem. Soc. Jpn. 91 (2018) 1596-1605.

324. Towards good correlation between fragment molecular orbital interaction 
energies and experimental IC50 for ligand binding: A case study of p38 MAP 
kinase. Y. Shenga, H. Watanabe, K. Maruyama, C. Watanabe, Y. Okiyama, T. Honma,
K. Fukuzawa, S. Tanaka, Comp. Str. Biotechn. J. 16 (2018) 421-434.

325. Development of the fragment-based COHSEX method for large and complex 
molecular systems. T. Fujita, Y. Noguchi, Phys. Rev. B 98 (2018) 205140.

326. Protein Residue Networks from Energetic and Geometric Data: Are They 
Identical? V. Sladek, H. Tokiwa, H. Shimano, Y. Shigeta, J. Chem. Theory 
Comput. 14 (2018) 6623-6631.

327. Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction 
Energies Generated by Fragment Molecular Orbital Calculations. T. Tokiwa, 
S. Nakano, Y. Yamamoto, T. Ishikawa, S. Ito, V. Sladek, K. Fukuzawa, 
Y. Mochizuki, H. Tokiwa, F. Misaizu, Y. Shigeta, J. Chem. Inf. Model. 59 (2019)
25-30.

328. Ligand chirality can affect histidine protonation of vitamin-D receptor: 
ab initio molecular orbital calculations in water. Y. Terauchi, R. Suzuki, 
R. Takeda, I. Kobayashi, A. Kittaka, M. Takimoto-Kamimura, N. Kurita,
J. Ster. Biochem. Mol. Biol. 186 (2019) 89-95.

329. Fragment Molecular Orbital Calculations with Implicit Solvent Based on the
Poisson-Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies.
Y. Okiyama, C. Watanabe, K. Fukuzawa, Y. Mochizuki, T. Nakano, S. Tanaka,
J. Phys. Chem. B 123 (2019) 957-973.

330. Specific interactions between 2-trans enoyl-acyl carrier protein reductase
and its ligand: Protein-ligand docking and ab initio fragment molecular orbital 
calculations. N. Phusi, R. Sato, T. Ezawa, S. Tomioka, C. Hanwarinroj,
B. Khamsri, P. Kamsri, A. Punkvang, P. Pungpo, N. Kurita, J. Mol. Graph. Model.
88 (2019) 299-308.

331. Characterising GPCR-ligand interactions using a fragment molecular 
orbital-based approach. A. Heifetz, T. James, M. Southey, I. Morao, M. Aldeghi, 
L. Sarrat, D. G. Fedorov, M. J. Bodkin, A. Townsend-Nicholson,
Curr. Opin. Struct. Biol. 55 (2019) 85-92.

332. Multithreaded parallelization of the energy and analytic gradient in the 
fragment molecular orbital method. V. Mironov, Y. Alexeev, D. G. Fedorov,
Int. J. Quant. Chem. 119 (2019) e25937.

333. The fragment molecular orbital method based on long-range corrected 
density-functional tight-binding. V. Q. Vuong, Y. Nishimoto, D. G. Fedorov, 
B. G. Sumpter, T. A. Niehaus, S. Irle, J. Chem. Theory Comput. 15 (2019) 
3008-3020.

334. Simulations of infrared and Raman spectra in solution using the fragment 
molecular orbital method. H. Nakata, D. G. Fedorov, Phys. Chem. Chem. Phys.
21 (2019) 13641-13652.

335. Molecular electrostatic potential and electron density of large systems in
solution computed with the fragment molecular orbital method. D. G. Fedorov,
A. Brekhov, V. Mironov, Y. Alexeev, J. Phys. Chem. A 123 (2019) 6281-6290.

336. Solvent screening in zwitterions analyzed with the fragment molecular 
orbital method. D. G. Fedorov, J. Chem. Theory Comput. 15 (2019) 5404-5416.

337. Lanthanide-induced conformational change of methanol dehydrogenase 
involving coordination change of cofactor pyrroloquinoline quinone. 
S. Tsushima, Phys. Chem. Chem. Phys. 21 (2019) 21979-21983.

338. Locating minimum energy crossings of different spin states using the 
fragment molecular orbital method. D. S. Kaliakin, D. G. Fedorov, Y. Alexeev,
S. A. Varganov, J. Chem. Theory Comput. 15 (2019) 6074-6084.

339. Investigation of hot spot region in XIAP inhibitor binding site by 
fragment molecular orbital method. H. Lim, X. Jin, J. Kim, S. Hwang, K. B. Shin,
J. Choi, K. Nam, K. T. No, Comp. Str. Biotechn. J. 17 (2019) 1217-1225.

340. Investigation of protein-protein interactions and hot spot region between 
PD-1 and PD-L1 by fragment molecular orbital method. H. Lim, J. Chun, X. Jin, 
J. Kim, J. Yoon, K. T. No, Sc. Rep. 9 (2019) 16727.

341. Hybrid distributed/shared memory model for the RI-MP2 method in the 
fragment molecular orbital framework. B. Q. Pham, M. S. Gordon, J. Chem. 
Theory Comput. 15 (2019) 5252-5258.

342. Interaction between calcite and adsorptive peptide analyzed by fragment
molecular orbital method. K. Kato, K. Fukuzawa, Y. Mochizuki, Jap. J. App. 
Phys. 58 (2019) 120906.

343. Fully quantum chemical treatment of chromophore? Protein interactions in 
phytochromes. R. Gonzalez, M. A. Mroginski, J. Phys. Chem. B 123 (2019)
9819-9830.

344. Recognition of repulsive and attractive regions of selected serotonin 
receptor binding site using FMO-EDA approach. P. Sliwa, R. Kurczab, R. Kafel, 
A. Drabczyk, J. Jaskowska, J. Mol. Mod. 25 (2019) 114.

345. A 3D-QSAR analysis of CDK2 inhibitors using FMO calculations and PLS 
regression. T. Yoshida, S. Hirono, Chem. Pharm. Bull. 67 (2019) 546-555.

346. Charge-transfer excited states in the donor/acceptor interface from 
large-scale GW calculations. T. Fujita, Y. Noguchi, T. Hoshi,
J. Chem. Phys. 151 (2019) 114109.

347. Assessing Peptide Binding to MHC II: An Accurate Semiempirical Quantum 
Mechanics Based Proposal. C. A. Ortiz-Mahecha, H. J. Bohórquez, W. A. Agudelo, 
M. A. Patarroyo, M. E. Patarroyo, C. F. Suárez, J. Chem. Inf. Model. 59 (2019) 
5148-5160.

348. Binding interaction analysis of RNA aptamer-Fc region of human 
immunoglobulin G using fragment molecular orbital calculation. H. Yoshida, 
K. Sato, T. Ishikawa, T. Sakamoto, K. Yamagishi, Chem. Phys. Lett. 738 (2020) 
136854.

349. Proposal of therapeutic curcumin derivatives for Alzheimer's disease 
based on ab initio molecular simulations. T. Shinzato, R. Sato, K. Suzuki, 
S. Tomioka, H. Sogawa, S. Shulga, Y. Blume, N. Kurita, Chem. Phys. Lett. 738 
(2020) 136883.

350. Binding sites of Zantrin inhibitors to the bacterial cell division protein
FtsZ: Molecular docking and ab initio molecular orbital calculations. H. Sogawa,
R. Sato, K. Suzuki, S. Tomioka, T. Shinzato, P. Karpov, S. Shulga, Y. Blume, 
N. Kurita, Chem. Phys. 530 (2020) 110603.

351. Development of the FMO/RI-MP2 fully analytic gradient using a 
hybrid-distributed/shared memory programming model. B. Q. Pham, M. S. Gordon,
J. Chem. Theory Comp. 16 (2020) 1039-1054.

352. FMOxFMO: elucidating excitonic interactions in the Fenna-Matthews-Olson 
complex with the fragment molecular orbital method. D. S. Kaliakin, H. Nakata,
Y. Kim, Q. Chen, D. G. Fedorov, L. V. Slipchenko, J. Chem. Theory Comp. 16 
(2020) 1175-1187.

353. Systematic interaction analysis of anti-human immunodeficiency virus 
type-1 neutralizing antibodies with high mannose glycans using fragment 
molecular orbital and molecular dynamics methods. M. Kusumoto, K. Ueno-Noto,
K. Takano, J. Comp. Chem. 41 (2020) 31-42.

354. Pair interaction energy decomposition analysis (PIEDA) and experimental 
approaches for investigating water interactions with hydrophilic and 
hydrophobic membranes. M. Maghami, A. Abdelrasoul, J. Mol. Graph. Mod. 96 
(2020) 107540.

355. Ab Initio Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) 
Simulations of (NH3)32 Cluster: Effects of Electron Correlation. M. Ninomiya, 
H. Doi, Y. Matsumoto, Y. Mochizuki, Y. Komeiji, Bull. Chem. Soc. Jpn. 93 (2020)
553-560.

356. Characterizing interhelical interactions of G-protein coupled receptors 
with the fragment molecular orbital method. A. Heifetz, I. Morao, M. M. Babu, 
T. James, M. W. Y. Southey, D. G. Fedorov, M. Aldeghi, M. J. Bodkin, 
A. Townsend-Nicholson, J. Chem. Theory Comput. 16 (2020) 2814-2824.

357. Fragmentation at sp2 carbon atoms in fragment molecular orbital method.
Y. Akinaga, K. Kato, T. Nakano, K. Fukuzawa, Y. Mochizuki, J. Comp. Chem.
41 (2020) 1416-1420.

358. Guiding medicinal chemistry with fragment molecular orbital (FMO) method.
A. Heifetz, T. James, M. Southey, M. J. Bodkin, S. Bromidge. 
In Quantum mechanics in drug discovery, A. Heifetz (Ed.), 
Methods in molecular biology, vol. 2114, pp. 37-48, Springer, New York, 2020.

359. Analyzing interactions with the fragment molecular orbital method. 
D. G. Fedorov, In Quantum mechanics in drug discovery, A. Heifetz (Ed.), 
Methods in molecular biology, vol. 2114, pp. 49-73, Springer, New York, 2020.

360. Geometry optimization, transition state search, and reaction path mapping 
accomplished with the fragment molecular orbital method. H. Nakata, 
D. G. Fedorov, In Quantum mechanics in drug discovery, A. Heifetz (Ed.), 
Methods in molecular biology, vol. 2114, pp. 87-104, Springer, New York, 2020.

361. Taking water into account with the fragment molecular orbital method. 
Y. Okiyama, K. Fukuzawa, Y. Komeiji, S. Tanaka,
In Quantum mechanics in drug discovery, A. Heifetz (Ed.), 
Methods in molecular biology, vol. 2114, pp. 105-122, Springer, New York, 2020.

362. Accurate scoring in seconds with the fragment molecular orbital and 
density-functional tight-binding methods. I. Morao, A. Heifetz, D. G. Fedorov, 
In Quantum mechanics in drug discovery, A. Heifetz (Ed.), 
Methods in molecular biology, vol. 2114, pp. 143-148, Springer, New York, 2020.

363. Analyzing GPCR-ligand interactions with the fragment molecular orbital 
(FMO) method. A. Heifetz, T. James, M. Southey, I. Morao, D. G. Fedorov, 
M. J. Bodkin, A. Townsend-Nicholson, 
In Quantum mechanics in drug discovery, A. Heifetz (Ed.), 
Methods in molecular biology, vol. 2114, pp. 163-176, Springer, New York, 2020.

364. Characterizing rhodopsin-arrestin interactions with the fragment molecular 
orbital (FMO) method. A. Heifetz, A. Townsend-Nicholson,
In Quantum mechanics in drug discovery, A. Heifetz (Ed.), 
Methods in molecular biology, vol. 2114, pp. 177-186, Springer, New York, 2020.

365. Characterizing protein-protein interactions with the fragment molecular 
orbital method. A. Heifetz, V. Sladek, A. Townsend-Nicholson, D. G. Fedorov, 
In Quantum mechanics in drug discovery, A. Heifetz (Ed.), 
Methods in molecular biology, vol. 2114, pp. 187-206, Springer, New York, 2020.

366. Protein ligand interaction analysis against new CaMKK2 inhibitors by use 
of X-ray crystallography and the fragment molecular orbital (FMO) method.
D. Takaya, H. Niwa, J. Mikuni, K. Nakamura, N. Handa, A. Tanaka, S. Yokoyama, 
T. Honma, J. Mol. Graph. Model. 99 (2020) 107599.

367. Three-body energy decomposition analysis based on the fragment molecular
orbital method. D. G. Fedorov, J. Phys. Chem. A 124 (2020) 4956-4971.

368. Machine learning prediction of inter-fragment interaction energies between
ligand and amino-acid residues on the fragment molecular orbital calculations 
for Janus kinase - inhibitor complex. S. Tokutomi, K. Shimamura, K. Fukuzawa,
S. Tanaka, Chem. Phys. Lett. 757 (2020) 137883.

369. Intermolecular interaction among Remdesivir, RNA and RNA-dependent RNA 
polymerase of SARS-CoV-2 analyzed by fragment molecular orbital calculation.
K. Kato, T. Honma, K. Fukuzawa, J. Mol. Graph. Model. 100 (2020) 107695.

370. Identification of correlated inter-residue interactions in protein complex
based on the fragment molecular orbital method. S. Tanaka C, Watanabe, 
T. Honma, K. Fukuzawa, K. Ohishi, T. Maruyama, J. Mol. Graph. Model. 100 (2020)
107650.

371. High-precision atomic charge prediction for protein systems using fragment
molecular orbital calculation and machine learning. K. Kato, T. Masuda, 
C. Watanabe, N. Miyagawa, H. Mizouchi, S. Nagase, K. Kamisaka, K. Oshima, 
S. Ono, H. Ueda, A. Tokuhisa, R. Kanada, M. Ohta, M. Ikeguchi, Y. Okuno, 
K. Fukuzawa, T. Honma, J. Chem. Inf. Model. 60 (2020) 3361-3368.

372. Fragment molecular orbital based interaction analyses on COVID-19 main 
protease-inhibitor N3 complex (PDB ID: 6LU7). R. Hatada, K. Okuwaki, 
Y. Mochizuki, Y. Handa, K. Fukuzawa, Y. Komeiji, Y. Okiyama, S. Tanaka,
J. Chem. Inf. Model. 60 (2020) 3593-3602

373. Revisiting the charge-transfer states at pentacene/C(60)interfaces with 
the GW/Bethe-Salpeter equation approach. T. Fujita, Y. Noguchi, T. Hoshi, 
Materials 13 (2020) 2728.

374. Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein 
interaction obtained by density functional tight binding fragment molecular 
orbital method. H. Lim, A. Baek, J. Kim, M. S. Kim, J. Liu, K. Nam, J. Yoon,
K. T. No, Sc. Rep. 10 (2020) 16862.

375. A novel method for analysis of the electrostatic complementarity of 
protein-protein interaction based on fragment molecular orbital method.
T. Ishikawa, Chem. Phys. Lett. 761 (2020) 138103.

376. Tunneling matrix element and tunneling pathways of protein electron 
transfer calculated with a fragment molecular orbital method.
H. Kitoh-Nishioka, Y. Shigeta, K. Ando, J. Chem. Phys. 153 (2020) 104104.

377. Characterization of PD-L1 binding sites by a combined FMO/GRID-DRY 
approach. R. Paciotti, M. Agamennone, C. Coletti, L. Storchi, 
J. Comp.-Aided Mol. Des. 34 (2020) 897-914.

378. Analytic first and second derivatives of the energy in the fragment 
molecular orbital method combined with molecular mechanics. H. Nakata, 
D. G. Fedorov, Int. J. Quantum Chem. 120 (2020) e26414.

379. Partition analysis for density-functional tight-binding. D. G. Fedorov,
J. Phys. Chem. A 124 (2020) 10346-10358.

380. Specific interactions between tau protein and curcumin derivatives:
Molecular docking and ab initio molecular orbital simulations. R. Sato,
S. Vohra, S. Yamamoto, K. Suzuki, P. Karpov, S. Shulga, Y. Blume, N. Kurita,
J. Mol. Graph. Model. 98 (2020) 107611.

381. Folding simulation of small proteins by dissipative particle dynamics (DPD)
with non-empirical interaction parameters based on fragment molecular orbital 
calculations. K. Okuwaki, H. Doi, K. Fukuzawa, Y. Mochizuki,
Appl. Phys. Expr. 13 (2020) 017002.

382. Interaction analyses of SARS-CoV-2 spike protein based on fragment 
molecular orbital calculations. K. Akisawa, R. Hatada, K. Okuwaki, 
Y. Mochizuki, K. Fukuzawa, Y. Komeiji, S. Tanaka, RSC Adv. 11 (2021) 3272-3279.
 
383. Statistical interaction analyses between SARS-CoV-2 main protease and 
inhibitor N3 by combining molecular dynamics simulation and fragment molecular 
orbital calculation. R. Hatada, K. Okuwaki, K. Akisawa, Y. Mochizuki, Y. Handa, 
K. Fukuzawa, Y. Komeiji, Y. Okiyama, S. Tanaka, Appl. Phys. Expr. 14 (2021) 
027003.

384. Fragment molecular orbital method as cluster expansion. S. Tanaka.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 3-14.

385. Recent development of the fragment molecular orbital method in GAMESS.
D. G. Fedorov.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 31-51.

386. The ABINIT-MP program. Y. Mochizuki, T. Nakano, K. Sakakura, Y. Okiyama, 
H. Watanabe, K. Kato, Y. Akinaga, S. Sato, J. Yamamoto, K. Yamashita, 
T. Murase, T. Ishikawa, Y. Komeiji, Y. Kato, N. Watanabe, T. Tsukamoto, 
H. Mori, K. Okuwaki, S. Tanaka, A. Kato, C. Watanabe, K. Fukuzawa.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 53-67.

387. PAICS: development of an open-source software of fragment molecular 
orbital method for biomolecule. T. Ishikawa.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 69-76.

388. Open-architecture program of fragment molecular orbital method for 
massive parallel computing (OpenFMO) with GPU acceleration. H. Kitoh-Nishioka,
H. Umeda, Y. Shigeta
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 77-90.

389. How to perform FMO calculation in drug discovery. K. Fukuzawa, 
C. Watanabe, Y. Okiyama, T. Nakano.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 93-125.

390. FMO drug design consortium. K. Fukuzawa, S. Tanaka, Y. Yagi, N. Kurita, 
N. Kawashita, K. Takaba, T. Honma.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 127-181.

391. Development of an automated FMO calculation protocol to construction of 
FMO database. C. Watanabe, H. Watanabe, Y. Okiyama, D. Takaya.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 183-203.

392. Application of FMO to ligand design: SBDD, FBDD, and protein-protein 
interaction. T. Ozawa, M. Ozawa.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 205-251.

393. Drug discovery screening by combination of X-ray crystal structure 
analysis and FMO calculation. M. Takimoto-Kamimura, N. Kurita.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 253-265.

394. Cooperative study combining X-ray crystal structure analysis and FMO 
calculation: interaction analysis of FABP4 inhibitors. U. Tagami, K. Takahashi.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 267-279.

395. Application of FMO for protein-ligand binding affinity prediction.
K. Takaba.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 281-294.

396. Elucidating the efficacy of clinical drugs using FMO. S. Arulmozhiraja, 
H. Tokiwa, H. Shimano.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 323-339.

397. Application of fragment molecular orbital calculations to functional 
analysis of enzymes. S. Nakano, S. Ito, H. Tokiwa.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 341-355.

398. AnalysisFMO toolkit: a PyMOL plugin for 3D-visualization of interaction 
energies in proteins (3D-VIEP) calculated by the FMO method. T. Tokiwa, 
S. Nakano, H. Tokiwa, Y. Shigeta.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 357-370.

399. FMO interfaced with molecular dynamics simulation. Y. Komeiji, 
T. Ishikawa. 
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 373-389.

400. Linear combination of molecular orbitals of fragments (FMO-LCMO) method: 
its application to charge transfer studies. H. Kitoh-Nishioka, R. Sato, 
Y. Shigeta, K. Ando.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 391-405.

401. Modeling of solid and surface. K. Kato, A. Hashimoto, E. Tamiya, 
K. Fukuzawa, Y. Ishikawa, Y. Mochizuki.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 407-424.

402. Development of the analytic second derivatives for the fragment molecular
orbital method. H. Nakata, D. G. Fedorov.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 425-458.

403. The FMO-DFTB method. Y. Nishimoto, S. Irle.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 459-485.

404. New methodology and framework information science-assisted analysis of 
FMO results for drug design. T. Takagi.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki, 
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 511-528.

405. Extension to multiscale simulations. K. Okuwaki, T. Ozawa, Y. Mochizuki.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki,
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 529-546.

406. FMO-based investigations of excited-state dynamics in molecular 
aggregates. T. Fujita, T. Hoshi.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki,
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 547-566.

407. Application of the fragment molecular orbital method to organic charge
transport materials in xerography: a feasibility study and a charge mobility
analysis. I. Fujino, D. G. Fedorov, K. Kitaura.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki,
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 567-587.

408. Multi-level parallelization of the fragment molecular orbital method in 
GAMESS. V. A. Mironov, Y. Alexeev, D. G. Fedorov, H. Umeda, S. Pruitt, 
A. Gaenko, M. S. Gordon.
In Recent advances of the fragment molecular orbital method, Y. Mochizuki,
S. Tanaka, K. Fukuzawa (Eds), Springer, Singapore, 2021, pp. 601-616.

409. FMODB: the world's first database of quantum mechanical calculations for 
biomacromolecules based on the fragment molecular orbital method. D. Takaya, 
C. Watanabe, S. Nagase, K. Kamisaka, Y. Okiyama, H. Moriwaki, H. Yuki,
T. Sato, N. Kurita, Y. Yagi, T. Takagi, N. Kawashita, K. Takaba, T. Ozawa, 
M. Takimoto-Kamimura, S. Tanaka, K. Fukuzawa, T. Honma,
J. Chem. Inf. Model. 61 (2021) 777-794.

410. Acceleration of environmental electrostatic potential using Cholesky 
decomposition with adaptive metric (CDAM) for fragment molecular orbital (FMO) 
method. Y. Okiyama, T. Nakano, C. Watanabe, K. Fukuzawa, Y. Komeiji, 
K. Segawa, Y. Mochizuki, Bull. Chem. Soc. Jap. 94 (2021) 91-96.

411. Prediction of lattice energy of benzene crystals: a robust theoretical 
approach.  A. L. P. Nguyen, T. G. Mason, B. D. Freeman, E. I. Izgorodina,
J. Comp. Chem 42 (2021) 248-260.

412. Proposal of novel inhibitors for vitamin-D receptor: Molecular docking, 
molecular mechanics and ab initio molecular orbital simulations.
S. Nakamura, R. Saito, S. Yamamoto, Y. Terauchi, A. Kittaka, 
M. Takimoto-Kamimura, N. Kurita, Biophys. Chem. 270 (2021) 106540.

413. The fragment molecular orbital method combined with density-functional 
tight-binding and periodic boundary conditions. Y. Nishimoto, D. G. Fedorov,
J. Chem. Phys. 154 (2021) 111102.

414. Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical 
hot spot and epitope analyses. C. Watanabe, Y. Okiyama, S. Tanaka, K. Fukuzawa,
T. Honma, Chem. Sci. 12 (2021) 4722-4739.

415. Partitioning of the vibrational free energy. D. G. Fedorov, J. Phys. Chem.
Lett. 12 (2021) 6628-6633.

416. Electron density from the fragment molecular orbital method combined with
density-functional tight-binding. D. G. Fedorov, Chem. Phys. Lett. 780 (2021)
138900.

417. Intermolecular interaction analyses on SARS-CoV-2 spike protein receptor 
binding domain and human angiotensin-converting enzyme 2 receptor-blocking 
antibody/peptide using fragment molecular orbital calculation.
K. Watanabe, C. Watanabe, T. Honma, Y.-S. Tian, Y. Kawashima, N. Kawashita, 
T. Takagi, K. Fukuzawa, J. Phys. Chem. Lett. 12 (2021) 4059-4066.

418. Computational ab initio interaction analyses between neutralizing antibody
and SARS-CoV-2 variant spike proteins using the fragment molecular orbital 
method. K. Watanabe, C. Watanabe, T. Honma, Y.-S. Tian, Y. Kawashima, N. 
Kawashita, K. Fukuzawa, T. Takagi, Bull. Chem. Soc. Jap. 94 (2021) 1794-1798.

419. Dynamic cooperativity of ligand-residue interactions evaluated with the 
fragment molecular orbital method. S. Tanaka, S. Tokutomi, R. Hatada, 
K. Okuwaki, K. Akisawa, K. Fukuzawa, Y. Komeiji, Y. Okiyama, Y. Mochizuki,
J. Phys. Chem. B 125 (2021) 6501-6512.

420. Proposal of novel natural inhibitors of severe acute respiratory syndrome 
coronavirus 2 main protease: Molecular docking and ab initio fragment molecular
orbital calculations. D. Shaji, S. Yamamoto, R. Saito, R. Suzuki, S. Nakamura,
N. Kurita, Biophys. Chem. 275 (2021) 106608.

421. Density-matrix based scheme of basis selection for linear combination of 
fragment molecular orbitals. Y. Okiyama, Y. Mochizuki, M. Yamanaka, S. Tanaka, 
J. Phys. Soc. Jpn. 90, 064301 (2021).

422. Proposal of novel potent inhibitors against androgen receptor based on ab 
initio molecular orbital calculations. S. Nakamura, R. Saito, S. Yamamoto,
I. Kobayashi, R. Takeda, R. Suzuki, K. Kawai, M. Takimoto-Kamimura, N. Kurita,
J. Mol. Graph. Model. 105 (2021) 107873.

423. Quantum mechanics helps uncover atypical recognition features in the 
flavin mononucleotide riboswitch. I. Deb, H. Wong, C. Tacubao, A. T. Frank,
J. Phys. Chem. B 125 (2021) 8342-8350.

424. Quantum-mechanical structure optimization of protein crystals and 
analysis of interactions in periodic systems. T. Nakamura, T. Yokaichiya, 
D. G. Fedorov, J. Phys. Chem. Lett. 12 (2021) 8757-8762.

425. Energy decomposition analysis of the adhesive interaction between an 
epoxy resin layer and a silica surface. C. Higuchi, K. Yoshizawa,
Langmuir 37 (2021) 8417-8425.

426. Visualization of the interfacial electrostatic complementarity: a method 
for analysis of protein-protein interaction based on ab initio quantum 
chemical calculations. H. Ozono, T. Ishikawa, J. Chem. Theory Comp. 17 (2021)
5600-5610.

427. Special features of COVID-19 in the FMODB: fragment molecular orbital 
calculations and interaction energy analysis of SARS-CoV-2-related proteins.
K. Fukuzawa, K. Kato, C. Watanabe, Y. Kawashima, Y. Handa, A. Yamamoto, 
K. Watanabe, T. Ohyama, K. Kamisaka, D. Takaya, T. Honma, J. Chem. Inf. 
Model. 61 (2021) 4594-4612.

428. Hot spot analysis of YAP-TEAD protein-protein interaction using the 
fragment molecular orbital method and its application for inhibitor discovery.
J. Kim, H. Lim, S. Moon, S. Y. Cho, M. Kim, J. H. Park, H. W. Park, K. T. No,
Cancers 13 (2021) 4246.

429. Evaluation of selective COX-2 inhibition and in silico study of kuwanon 
derivatives isolated from morus alba. S.-H. Baek, S. Hwang, T. Park, 
Y.-J. Kwon, M. Cho, D. Park, Sc. Rep. 22 (2021) 3659.

430. On the question of steric repulsion versus noncovalent attractive 
interactions in chiral phosphoric acid catalyzed asymmetric reactions. 
S. Tribedi, K. Kitaura, T. Nakajima, R. B. Sunoj, Phys. Chem. Chem. Phys.
23 (2021) 18936-18950.

431. Interaction analysis on the SARS-CoV-2 spike protein receptor binding 
domain using visualization of the interfacial electrostatic complementarity.
T. Ishikawa, H. Ozono, K. Akisawa, R. Hatada, K. Okuwaki, Y. Mochizuki,
J. Phys. Chem. Lett. 12 (2021) 11267-11272.
 
432. Fragment-based excited-state calculations using the GW approximation and 
the Bethe-Salpeter equation. T. Fujita, Y. Noguchi, J. Phys. Chem. A 125 
(2021) 10580-10592.

433. Ligand binding: evaluating the contribution of the water molecules network
using the fragment molecular orbital method. I. Lukac, P. G. Wyatt, 
I. H. Gilbert, Fabio Zuccotto, J. Comp.-Aid. Mol. Des. 35 (2021) 1025-1036.

434. Proposal of selective inhibitor for bacterial zinc metalloprotease: 
Molecular mechanics and ab initio molecular orbital calculations.
K. Imai, R. Saito, T. Ezawa, S. Sugiyama, I. Sylte, N. Kurita, J. Mol. Graph. 
Model. 110 (2022) 108047.

435. Fragment molecular orbital calculations for biomolecules. K. Fukuzawa, 
S. Tanaka, Curr. Opin. Struct. Biol. 72 (2022) 127-134.

436. Analysis of guest adsorption on crystal surfaces based on the fragment 
molecular orbital method. T. Nakamura, T. Yokaichiya, D. G. Fedorov,
J. Phys. Chem. A 126 (2022) 957-969.

437. Free energy decomposition analysis based on the fragment molecular orbital
method. D. G. Fedorov, T. Nakamura, J. Phys. Chem. Lett. 13 (2022) 1596-1601.

438. Computational approach to elucidate the formation and stabilization 
mechanism of amorphous formulation using molecular dynamics simulation and 
fragment molecular orbital calculation.  X. Mai, K. Higashi, K. Fukuzawa, 
K. Ueda, K. Kadota, Y. Tozuka, E. Yonemochi, K. Moribe, Int. J. Pharmaceutics 
615 (2022) 121477

439. Identification of key stabilizing interactions of amyloid-beta oligomers 
based on fragment molecular orbital calculations on macrocyclic beta-hairpin 
peptides. R. Firouzi, B. Noohi, Prot.: Str. Funct. Bioinf. 90 (2022)
229-238.

440. Specific interactions between the alkaline protease of P. aeruginosa and 
its natural peptide inhibitor: ab initio molecular simulations. R. Saito, 
K. Imai, S. Yamamoto, T. Ezawa, S. Sugiyama, L. S. M. Evenseth, I. Sylte,
N. Kurita, J. Mol. Model. 28 (2022) 10.

441. Residue interactions affecting the deprotonation of internal guanine 
moieties in oligodeoxyribonucleotides, calculated by FMO methods. 
J. C. González-Olvera, A. Zamorano-Carrillo, G. Arreola-Jardón, R. C. Pless,
J. Mol. Model. 28 (2022) 43.

442. Evaluation of protein descriptors in computer-aided rational protein 
engineering tasks and its application in property prediction in SARS-CoV-2 
spike glycoprotein. H. Lim, H.-N. Jeon, S. Lim, Y. Jang, T. Kim, H. Cho, 
J.-G. Pan, K. T. No, Comp. Str. Biotechn. J. 20 (2022) 788-798.

443. Towards a quantitative description of excitonic couplings in  
photosynthetic pigment-protein complexes: quantum chemistry driven multiscale 
approaches. C. Friedl, D. G. Fedorov, T. Renger, Phys. Chem. Chem. Phys. 24
(2022) 5014-5038.

444. The catalytic activity and adsorption in faujasite and ZSM-5 zeolites:  
the role of differential stabilization and charge delocalization.
T. Nakamura, D. G. Fedorov, Phys. Chem. Chem. Phys. 24 (2022) 7739-7747.

445. Halogenated baicalein as a promising antiviral agent toward SARS-CoV-2 
main protease. K. Hengphasatporn, P. Wilasluck, P. Deetanya, K. Wangkanont, 
W. Chavasiri, P. Visitchanakun, A. Leelahavanichkul, W. Paunrat, 
S. Boonyasuppayakorn, T. Rungrotmongkol, S. Hannongbua, Y. Shigeta,
J. Chem. Inf. Model. 62 (2022) 1498-1509.

446. Polarization energies in the fragment molecular orbital method.
D. G. Fedorov, J. Comp. Chem. 43 (2022) 1094-1103.

447. Interaction analysis of the spike protein of delta and omicron variants 
of SARS-CoV-2 with hACE2 and eight monoclonal antibodies using the fragment 
molecular orbital method. S. Hwang, S.-H. Baek, D. Park, J. Chem. Inf. Model. 
62 (2022) 1771-1782.

448. Identification of novel natural product inhibitors against matrix 
metalloproteinase 9 using quantum mechanical fragment molecular orbital-based 
virtual screening methods. H. Lim, H. Hong, S. Hwang, S. J. Kim, S. Y. Seo,
K. T. No, Int. J. Mol. Sci. 23 (2022) 4438.

449. A study on the effect of the substituent against PAK4 inhibition using 
in silico methods. H. R. Yoon, C. C. Chai, C. H. Kim, N. S. Kang,
Int. J. Mol. Sci. 23 (2022) 3337.

450. Collective residue interactions in trimer complexes of SARS-CoV-2 spike 
proteins analyzed by fragment molecular orbital method, K. Okuwaki, K. Akisawa,
R. Hatada, Y. Mochizuki, K. Fukuzawa, Y. Komeiji, S. Tanaka, Appl. Phys. Expr. 
15 (2022) 017001.

451. A double exponential coupled cluster theory in the fragment molecular 
orbital framework. A. Chakraborty, S. Tribedi, R. Maitra, J. Chem. Phys. 156 
(2022) 244117.

452. Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 
inhibitors by dynamically averaged fragment molecular orbital-based interaction
energy. K. Takaba, C. Watanabe, A. Tokuhisa, Y. Akinaga, B. Ma, R. Kanada, 
M. Araki, Y. Okuno, Y. Kawashima, H. Moriwaki, N. Kawashita, T. Honma, 
K. Fukuzawa, S. Tanaka, J. Comp. Chem. 43 (2022) 1362-1371.

453. Evaluating the correlation of binding affinities between isothermal 
titration calorimetry and fragment molecular orbital method of estrogen 
receptor beta with diarylpropionitrile (DPN) or DPN derivatives. C. Handa, 
Y. Yamazaki, S. Yonekubo, N. Furuya, T. Momose, T. Ozawa, T. Furuishi,
K. Fukuzawa, E. Yonemochi, J. Ster. Biochem. Mol. Biol. 222 (2022) 106152.

454. Hotspot identification and drug design of protein-protein interaction 
modulators using the fragment molecular orbital method. S. Monteleone, 
D. G. Fedorov, A. Townsend-Nicholson, M. Southey, M. Bodkin, A. Heifetz,
J. Chem. Inf. Model. 62 (2022) 3784-3799.

455. Quantification and neutralization of the interfacial electrostatic 
potential and visualization of the dispersion interaction in visualization of 
the interfacial electrostatic complementarity. H. Ozono, K. Mimoto, 
T. Ishikawa, J. Phys. Chem. B 126 (2022) 8415-8426.

456. Interspecies comparison of interaction energies between photosynthetic 
protein RuBisCO and 2CABP ligand. M. Fujii, S. Tanaka, Int. J. Mol. Sci. 
23 (2022) 11347.

457. The importance of charge transfer and solvent screening in the 
interactions of backbones and functional groups in amino acid residues and 
nucleotides. V. Sladek, D. G. Fedorov, Int. J. Mol. Sci. 23 (2022) 13514.

458. The FMO2 analysis of the ligand-receptor binding energy: the 
biscarbene-gold(I)/DNA G-quadruplex case study. R. Paciotti, C. Coletti, 
A. Marrone, N. Re, J. Comput. Aided Mol. Des. 36 (2022) 851-866.

459. Parametrized quantum-mechanical approaches combined with the fragment 
molecular orbital method. D. G. Fedorov, J. Chem. Phys. 157 (2022) 231001.

460. Scaling correlated fragment molecular orbital calculations on Summit.
G. Barca, C. Snowdon, J. Vallejo, F. Kazemian, A. P. Rendell, M. S. Gordon,
Proc. Supercomputing 2022, Dallas, 2022, pp. 72-85.

461. Complete guide to the fragment molecular orbital method in GAMESS.
D. G. Fedorov, World Scientific, Singapore, 2023.

462. Protein-protein interaction modelling with the fragment molecular orbital 
method. S. Tanaka, in K. Tsumoto, D. Kuroda (Eds.) Computer-aided antibody 
design. Methods in molecular biology, vol. 2552, Humana, New York, 2023, 
pp. 295-305.

463. System truncation accelerates binding affinity calculations with the 
fragment molecular orbital method: A benchmark study. S. Nakamura, T. Akaki, 
K. Nishiwaki, M. Nakatani, Y. Kawase, Y. Takahashi, I. Nakanishi, J. Comp.
Chem. 44 (2023) 824-831.

464. Long-range corrected fragment molecular orbital density functional 
tight-binding method for excited states in large molecular systems.
R. Einsele, J. Hoche, R. Mitrić, J. Chem. Phys. 158 (2023) 044121.

465. Structure-based drug design of novel M. tuberculosis InhA inhibitors based
on fragment molecular orbital calculations. N. Phusi, Y. Hashimoto, N. Otsubo, 
K. Imai, P. Thongdee, D. Sukchit, P. Kamsri, A. Punkvang, K. Suttisintong, 
P. Pungpo, N. Kurita, Comp. Biol. Med. 152 (2023) 106434.

466. Analytic gradient for time-dependent density functional theory combined 
with the fragment molecular orbital method. H. Nakata, D. G. Fedorov,
J. Chem. Theory Comp. 19 (2023) 1276-1285.

467. Dynamical interaction analysis of proteins by a random forest-fragment 
molecular orbital (RF-FMO) method and application to Src tyrosine kinase.
Y. Yamamoto, S. Nakano, Y. Shigeta, Bull. Chem. Soc. Jap. 96 (2023) 42-47.

468. Quantum chemical interaction analysis between SARS-CoV-2 main protease and
ensitrelvir compared with its initial screening hit. C. Watanabe, S. Tanaka, 
Y. Okiyama, H. Yuki, T. Ohyama, K. Kamisaka, D. Takaya, K. Fukuzawa, T. Honma,
J. Phys. Chem. Lett. 14 (2023) 3609-3620.

469 SophosQM: accurate binding affinity prediction in compound optimization.
R. Guareschi, I. Lukac, I. H. Gilbert, F. Zuccotto, ACS Omega 8 (2023)
15083-15098.

470. Fragment molecular orbital based affinity prediction toward pyruvate 
dehydrogenase kinases: insights into the charge transfer in hydrogen bond 
networks. T. Akaki, S. Nakamura, K. Nishiwaki, I. Nakanishi.
Chem. Pharm. Bull. 71 (2023) 299-306.

471. Proposal of novel ApoE4 inhibitors from the natural spice Cinnamon for 
the treatment of Alzheimer's disease: Ab initio molecular simulations.
D. Shaji, A. Das, R. Suzuki, Y. Nagura, H. Sabishiro, N. Kurita, Biophys. Chem.
296 (2023) 106990.

472. Theoretical study on the regulating mechanism of the transition between 
the open-closed state of hCtBP2: a combined molecular dynamics and quantum 
mechanical interaction analysis. Y. Yamamoto, Y. Shigeta, Chem. Lett. 52 (2023)
120-123.

473. Interactions of opicapone in the binding pocket of catechol 
o-methyltransferase: a crystallographic study and fragment molecular orbital 
analyses. K. Takebe, M. Suzuki, T. Kuwada-Kusunose, S. Shirai, K. Fukuzawa, 
T. Takamiya, N. Uzawa, H. Iijima, J. Chem. Inf. Model. 63 (2023) 4468-4476.

474. How E-, L-, and P-selectins bind to sLex and PSGL-1: a quantification of 
critical residue interactions. V. Sladek, P. Šmak, I. Tvaroška,
J. Chem. Inf. Model. 63 (2023) 5604-5618.

475. Dissipative particle dynamics simulation for peptoid nanosheet with 
non-empirical parameter set. Y. Tachino, K. Okuwaki, H. Doi, K. Akisawa, 
Y. Mochizuki, Jap. J. Appl. Phys. 62 (2023) 090902.

476. Site-specific ionization potentials and electron affinities in large 
molecular systems at coupled cluster level. D. G. Fedorov,
J. Phys. Chem. A 127 (2023) 9357-9364.

477. The C-terminal tail of Rad17, iVERGE, binds the 9-1-1 complex 
independently of AAA+ ATPase domains to provide another clamp-loader interface,
Y. Fukumoto, T. Hoshino, Y. Nakayama, Y. Ogra, DNA Repair 130 (2023) 103567.

478. Development of reverse mapping system bridging dissipative particle 
dynamics and fragment molecular orbital calculation. K. Okuwaki, H. Doi, 
T. Ozawa, Y. Mochizuki, Jap. J. Appl. Phys. 62 (2023) 110902.

479. Probing RNA-small molecule interactions using biophysical and 
computational approaches. A. Shino, M. Otsu, K. Imai, K. Fukuzawa, 
E. C. Morishita, ACS Chem. Biol. 18 (2023) 2368-2376.

480. In silico design of natural inhibitors of ApoE4 from the plant moringa 
oleifera: molecular docking and ab initio fragment molecular orbital 
calculations. D. Shaji, Y. Nagura, H. Sabishiro, R. Suzuki, N. Kurita,
Molecules 28 (2023) 8035.

481. Leveraging the Fragment Molecular Orbital Method to Explore the PLK1 
Kinase Binding Site and Polo-Box Domain for Potent Small-Molecule Drug Design.
H. Jin, J. Kim, O. Lee, H. Kim, K. T. No, Int. J. Mol. Sci. 24 (2023), 15639.

482. Binding free energy calculation based on the fragment molecular orbital 
method and its application in designing novel SHP-2 allosteric inhibitors.
Z. Yuan, X. Chen, S. Fan, L. Chang, L. Chu, Y. Zhang, J. Wang, S. Li, J. Xie,
J. Hu, R. Miao, L. Zhu, Z. Zhao, H. Li, S. Li, Int. J. Mol. Sci. 25 (2024) 671.

483. Quantum-chemical analyses of interactions for biochemical applications. 
D. G. Fedorov, In Computational drug discovery: methods and applications,
V. Poongavanam, V. Ramaswamy (Eds.), Wiley, 2024, pp. 183-210.

484. Fragment molecular orbital-based variational quantum eigensolver for 
quantum chemistry in the age of quantum computing. H. Lim, D. H. Kang, 
J. Kim, A. Pellow-Jarman, S. McFarthing, R. Pellow-Jarman, H.-N. Jeon, 
B. Oh, J.-K. K. Rhee, K. T. No, Sc. Rep. 14 (2024) 2422.

485. FMO-guided design of darunavir analogs as HIV-1 protease inhibitors.
H. Chuntakaruk, K. Hengphasatporn, Y. Shigeta, C. Aonbangkhen, V. S. Lee, 
T. Khotavivattana, T. Rungrotmongkol, S. Hannongbua, Sc. Rep. 14 (2024) 3639.

486. Analysis of site energies and excitonic couplings: the role of symmetry 
and polarization. D. G. Fedorov, J. Phys. Chem. A 128 (2024) 1154-1162.

487. Enhancement of energy decomposition analysis in fragment molecular orbital
calculations. S. Matsuoka, K. Sakakura, Y. Akinaga, K. Akisawa, K. Okuwaki, 
H. Doi, Y. Mochizuki, J. Comp. Chem. 45 (2024) 898-902.

488. Prediction of binding pose and affinity of nelfinavir, a SARS-CoV-2 main 
protease repositioned drug, by combining docking, molecular dynamics, and 
fragment molecular orbital calculations. Y. Handa, K. Okuwaki, Y. Kawashima, 
R. Hatada, Y. Mochizuki, Y. Komeiji, S. Tanaka, T. Furuishi, E. Yonemochi, 
T. Honma, K. Fukuzawa, J. Phys. Chem. B 128 (2024) 2249-2265.