Secondary FMO references
(that is, where FMO is not used as the main method/subject, or for some other
reasons).

1. Y. Inadomi, T. Nakano, K. Kitaura, U. Nagashima, Increased Efficiency of 
Parallel Calculations of Fragment Molecular Orbitals by Using Fine-Grained 
Parallelization on a HITACHI SR8000 Supercomputer, Lecture Notes in
Computer Science", Springer, Berlin, Vol. 2110,
High-Performance Computing and Networking, Springer, Berlin, 2001, p. 569.
2. Y. Komeiji, Y. Inadomi, T. Nakano, PEACH 4 with ABINIT-MP: a general 
platform for classical and quantum simulations of biological molecules,
Comput. Biol. Chem. 28 (2004) 155-161.
3. Increased Efficiency of Parallel Calculations of Fragment Molecular
Orbitals by Using Fine-Grained Parallelization on a HITACHI SR8000
Supercomputer, Y. Inadomi, T. Nakano, K. Kitaura, U. Nagashima,
in "Lecture Notes in Computer Science", Vol. 2110/2001, Springer, Berlin, 
2004, p. 569. ISBN: 978-3-540-42293-8.
4. Electronic properties of DNA by DFT calculations based on fragment molecular
orbital method, Y. Sengoku, M. Matsuoka, S.-I. Sugiki, S. Tanaka, N. Kurita,
H. Sekino, J. Comput. Aided Chem. 5 (2004) 1-8.
5. Common Semiopen Conformations of Mg2+-Free Ras, Rho, Rab, Arf, and Ran
Proteins Combined with GDP and Their Similarity with GEF-Bound Forms
Mori, K.; Hata, M.; Neya, S.; Hoshino, T. J. Am. Chem. Soc. 127 (2005), 
15127-15137.
6. Vitamin D Receptor: Ligand Recognition and Allosteric Network,
K. Yamamoto, D. Abe, N. Yoshimoto, M. Choi, K. Yamagishi, H. Tokiwa, 
M. Shimizu, M. Makishima, and S. Yamada, J. Med. Chem. 49 (2006) 1313-1324.
7. Computational Simulations of HIV-1 Proteases-Multi-drug Resistance Due to
Nonactive Site Mutation L90M, Ode, H.; Neya, S.; Hata, M.; Sugiura, W.; 
Hoshino, T., J. Am. Chem. Soc. 128, (2006), 7887-7895.
8. Drug discovery using grid technology, H. Goto, S. Obata, T. Kamakura, 
N. Nakayama, M. Sato, Y. Nakajima, U. Nagashima, T. Watanabe, Y. Inadomi, 
M. Ito, T. Nishikawa, T. Nakano, L. Nilsson, S. Tanaka, K. Fukuzawa, Y. Inagaki,
M. Hamada, H. Chuman, in "Modern methods for theoretical physical chemistry of 
biopolymers", E. B. Starikov, J. P. Lewis, S. Tanaka, Eds., pp 227-248, 
Elsevier, Amsterdam, 2006.
9. Theoretical prediction of optical absorption maxima for photosensory 
receptor mutants, K. Kawaguchi, T. Yamato, Chem. Phys. Lett. 430 (2006) 386. 
10. Aggregation mechanism of polyglutamine diseases revealed using quantum 
chemical calculations, fragment molecular orbital calculations, molecular 
dynamics simulations, and binding free energy calculations, K. Tsukamoto, 
H. Shimizu, T. Ishida, Y. Akiyama, N. Nukina, J. Mol. Str. (THEOCHEM) 778 
(2006), 85-95.
11. Computational Analysis of the Proton Translocation from Asp96 to Schiff
Base in Bacteriorhodopsin, Sato, Y.; Hata, M.; Neya, S.; Hoshino, T.
J. Phys. Chem. B. (2006), 110, 22804-22812. 
12 . T. Sakurai, Y. Kodaki, H. Tadano, H. Umeda, Y. Inadomi, T. Watanabe, U.
Nagashima, A Master-Worker Type Eigensolver for Molecular Orbital
Computations, in Lecture Notes in Computer Science, vol. 4699, 
Applied Parallel Computing. State of the Art in Scientific
Computing, Springer Berlin, 2007, pp. 617-625.
13. M. Aoyagi, 2007, Grid Enabling of Nano-Science Applications in NAREGI,
in IFIP International Federation for Information Processing, Volume 239, 
Grid-Based Problem Solving Environments, eds. Gaffney.
P. W., Pool, J.C.T., (Boston: Springer), pp. 393-394.
14. The Predictive Accuracies of Spectroscopic Parameters in Biological
Macromolecules by Fragment MO Method, Y. Sengoku, S. Miyahara, H. Wakabayashi
H. Sekino, J. Comput. Aided Chem. 8 (2007) pp.85-91.
15. Evaluation of NMR Chemical Shift by Fragment Molecular Orbital
Method, H. Sekino, N. Matsumura, Y. Sengoku, Comput. Lett. 3 (2007) 423-430.
16. Fragmentation position dependency of the total energy and atomic charge
difference between the fragment MO method and conventional ab initio SCF-MO 
method. A case of (-)-epicatechin gallate with STO-3G basis set, K. Tamura, 
Y. Inadomi, U. Nagashima, Bull. Chem. Soc. Jpn. 80 (2007) 721-723.
17. Difference in the potential energy surfaces from the fragment MO method
and conventional ab initio SCF-MO method. A case of a surface for ring
rotation of (-)-epicatechin gallate using the STO-3G basis set,
K. Tamura, T. Watanabe, T. Ishimoto, U. Nagashima, Bull. Chem. Soc. Jpn. 80, 
(2007) 1939-1941.
18.  Ab initio MO-MD simulation based on the fragment MO method. A case of
(-)-epicatechin gallate with STO-3G basis set, K. Tamura, T. Watanabe, T.
Ishimoto, U. Nagashima, Bull. Chem. Soc. Jpn. 81 (2008), 110-112.
19.  FMO-MO method as an initial guess generation for SCF calculation: Case of
(-)-epicatechin gallate, K. Tamura, T. Watanabe, T. Ishimoto, H. Umeda, 
Y. Inadomi, U. Nagashima, Bull. Chem. Soc. Jpn. 81 (2008) 254-256.
20. Interaction of HIV-1 aspartic protease with its inhibitor, by molecular
dynamics and ab initio fragment molecular orbital method, K. Koyano, 
T. Nakano, J. Synchr. Rad. 15 (2008) 239-242.
21. Binding Interaction Analysis of the Active Site and Its Inhibitors for
Neuraminidase (N1 Subtype) of Human Influenza Virus by the Integration of
Molecular Docking, FMO Calculation and 3D-QSAR CoMFA Modeling,
Zhang, Q.; Yang, J.; Liang, K.; Feng, L.; Li, S.; Wan, J.; Xu, X.; Yang, G.;
Liu, D.; Yang, S. J. Chem. Inf. Model 48 (2008) 1802-1812.  
22. GridFMO - Quantum chemistry of proteins on the Grid. T. Ikegami, J. Maki, 
T. Takami, Y. Tanaka, M. Yokokawa, S. Sekiguchi, M. Aoyagi,
Proc. 8th IEEE/ACM International Conference on Grid Computing, Austin, 2007,
50-57. 
23. Multi-physics extension of OpenFMO framework. T. Takami, J. Maki, J. Ooba,
Y. Inadomi, H. Honda, R. Susukita, K. Inoue, T. Kobayashi, R. Nogita, M. Aoyagi,
Proc. International Conference on Computational Methods in Science and 
Engineering, Corfu, Greece, 2007, AIP Conf. Proc. Vol. 2, 122-125,
Part A-B.
24. Ab initio FMO-MD method reimplemented and applied to pure water. 
Y. Komeiji, T. Ishikawa, Y. Mochizuki, H. Yamataka, T. Nakano,
Proc. International Conference on Computational Methods in Science and
Engineering, Corfu, Greece, 2007, AIP Conf. Proc. Vol. 2,
1261-1264, Part A-B. 
25. Structural stability analysis of the intermediates in the folding pathway
of human telomeric hybrid-1 G-quadruplex based on fragment molecular orbital
method. H. Yagi, T. Mashimo, Y. Sannohe, H. Sugiyama, Nucl. Acids Symp. Ser. 
52 (2008) 161-162.
26. Probing protein environment in an enzymatic process: all-electron
quantum chemical analysis combined with ab initio quantum mechanical/molecular 
mechanical modeling of chorismate mutase. T. Ishida, J. Chem. Phys. 129 (2008)
125105.
27. Accurate Methods for Large Molecular Systems.
M. S. Gordon, J. M. Mullin, S. R. Pruitt, L. B. Roskop, L. V. Slipchenko and 
J. A. Boatz, J. Phys. Chem. B 113 (2009) 9646-9663.
28. Ab initio base fragment molecular orbital studies of influenza viral
hemagglutinin HA1 full-domains in complex with sialoside receptors.
T. Sawada, T. Hashimoto, H. Tokiwa, T. Suzuki, H. Nakano, H. Ishida, M. Kiso,
Y. Suzuki, J Mol Genet Med. 3 (2009) 133-142.
29. Theoretical study of hydration models of trivalent rare-earth ions using
model core potentials. T. Fujiwara, H. Mori, Y. Mochizuki, H. Tatewaki, E.
Miyoshi, J. Mol. Str. (THEOCHEM) 949 (2010) 28-35.
30. Effects of Point Mutation on Enzymatic Activity: Correlation between
Protein Electronic Structure and Motion in Chorismate Mutase Reaction.
T. Ishida, J. Am. Chem. Soc., 132 (2010) 7104-7118.
31. Effective Fragment Molecular Orbital Method: A Merger of the Effective
Fragment Potential and Fragment Molecular Orbital Methods. C. Steinmann, 
D. G. Fedorov, J. H. Jensen, J. Phys. Chem. A 114 (2010) 8705-8712.
32. Ab initio fragment molecular orbital calculations on the specific
interactions between human, mouse and rat PPARagr and GW409544.
M. Hayakawa, T. Ohyama, Y. Yamaguchi, S. Iwabuchi, T. Nakagawa, T. Nakajima, 
N. Kurita. Mol. Sim. 36 (2010) 644-656. 
33. Molecular tailoring approach in conjunction with MP2 and Ri-MP2 codes: A
comparison with fragment molecular orbital method. A. P. Rahalkar, M. Katouda, 
S. R. Gadre, S. Nagase, J. Comp. Chem. 31 (2010) 2405-2418.
34. Folding Pathways of Human Telomeric Type-1 and Type-2 G-Quadruplex
Structures. T. Mashimo, H. Yagi, Y. Sannohe, A. Rajendran, H. Sugiyama,
J. Am. Chem. Soc. 132 (2010) 14910-14918.
35. 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.
36. Compound Design by Fragment-Linking. O. Ichihara, J. Barker, R. J. Law,
M. Whittaker, Mol. Inf. 30 (2011) 298-306.
37. Book Review: The Fragment Molecular Orbital Method:
Practical Applications to Large Molecular Systems. L. Massa,
Int. J. Quantum Chem. 111 (2011) 3251.
38. Rational questing for potential novel inhibitors of FabK from Streptococcus
pneumoniae by combining FMO calculation, CoMFA 3D-QSAR modeling and virtual 
screening. Q. Zhang, C. Yu, J. Min, Y. Wang, J. He, Z. Yu, J. Mol. Model. 17 
(2011) 1483-1492.
39. Acceleration of a QM/MM-QMC simulation using GPU. Y. Uejima, T. Terashima,
R. Maezono, J. Comp. Chem. 32 (2011) 2264-2272.
40. Large scale quantum chemical calculation for drug discovery.
K. Kitaura, Yakugaku zasshi 131 (2011) 1163-1169.
41. Specific interactions and binding free energies between thermolysin and
dipeptides: Molecular simulations combined with Ab initio molecular orbital
and classical vibrational analysis. K. Dedachi, T. Hirakawa, S. Fujita,
M. T. H. Khan, I. Sylte, N. Kurita, J. Comp. Chem. 32 (2011) 3047-3057.
42. Model for the fast estimation of basis set superposition error in
biomolecular systems. J. C. Faver, Z. Zheng, K. M. Merz, Jr. J. Chem. Phys. 
135, 144110 (2011).
43. Structure-based rational design of novel hit compounds for pyruvate
dehydrogenase multienzyme complex E1 components from Escherichia coli.
Y. Ren, J. He, L. Feng, X. Liao, J. Jin, Y. Li, Y. Cao, J. Wan, H. He,
Bioorg. Med. Chem. 19 (2011) 7501-7506.
44. Fragmentation Methods: A Route to Accurate Calculations on Large Systems.
M. S. Gordon, D. G. Fedorov, S. R. Pruitt, L. V. Slipchenko,
Chem. Rev. 112 (2012) 632-672.
45. Structure and Dynamics of the 1-Hydroxyethyl-4-amino-1,2,4-triazolium
Nitrate High-Energy Ionic Liquid System. P. J. Carlson, S. Bose, D. W.
Armstrong, T. Hawkins, M. S. Gordon, J. W. Petrich, J. Phys. Chem. B 116
(2012) 503-512.
46. Discovery and Structure-Activity Relationship of Potent and Selective
Covalent Inhibitors of Transglutaminase 2 for Huntingtons Disease.
M. E. Prime, O. A. Andersen, J. J. Barker, M. A. Brooks, R. K. Y. Cheng, 
I. Toogood-Johnson, S. M. Courtney, F. A. Brookfield, C. J. Yarnold, 
R. W. Marston, P. D. Johnson, S. F. Johnsen, J. J. Palfrey, D. Vaidya, 
S. Erfan, O. Ichihara, B. Felicetti, S. Palan, A. Pedret-Dunn, S. Schaertl, 
I. Sternberger, A. Ebneth, A. Scheel, D. Winkler, L. Toledo-Sherman, 
M. Beconi, D. Macdonald, I. Munoz-Sanjuan, C. Dominguez, J. Wityak,
J. Med. Chem. 2012, 55, 1021-1046.