Publications in English

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Book chapters

  1. Mochizuki, Y., Nakano,T., Sakakura,K., Okiyama, Y., Watanabe, H., Kato, K., Akinaga, Y., Sato, S., Yamamoto, J., Yamashita, K., Murase, T., Ishikawa, T., Komeiji, Y., Kato, Y., Watanabe, N., Tsukamoto,T., Mori, H., Okuwaki, K., Tanaka, T., Kato, A., Watanabe, C., Fukuzawa, K. (2021) in "Recent Advances of the Fragment Molecular Orbital Method - Enhanced Performance and Applicability - (Mochizuki, Y., Tanaka, S., and Fukuzawa, K., eds.)," pp. 53-67. Springer Singapore. Chapter 4: The ABINIT-MP program.

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  2. Komeiji, Y., Ishikawa, T. (2021) in "Recent Advances of the Fragment Molecular Orbital Method - Enhanced Performance and Applicability - (Mochizuki, Y., Tanaka, S., and Fukuzawa, K., eds.)," pp. 379-388, Springer Singapore. Chapter 19: FMO interfaced with Molecular Dynamics simulation.

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  3. Okiyama, Y., Fukuzawa, K., Komeiji, Y., Tanaka, S. (2020) in "Quantum Mechanics in Drug Discovery (Heifetz, A., ed.)," Methods in Molecular Biology, vol. 2114, pp. 105-122, Humana Press, New York, NY. Taking Water into Account with the Fragment Molecular Orbital Method.

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  4. Komeiji, Y., Mochizuki, Y., Nakano, T., Mori, H. (2012) in "Molecular Dynamics - Theoretical Developments and Applications in Nanotechnology and Energy (Wang, L., ed.)," pp. 3-24. InTech, Rijeka, Kroatia. Chapter 1: Recent advances in fragment molecular orbital-based molecular dynamics (FMO-MD) simulations.

    [Open Access Book]

  5. Komeiji, Y. (2009) in "The Fragment Molecular Orbital method: practical applications to large molecular systems (Fedorov, D. G. & Kitaura, K, eds.)," pp. 119-132, CRC Press, London. Chapter 6 FMO-MD: An ab initio-based molecular dynamics of large systems.

    [Publisher]

  6. Komeiji, Y. (2001) In "Recent Research Developments in Protein Engineering 1," pp. 1-20, Research Signpost, India. Biomolecular simulation using the PEACH software.

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Refereed journal articles

  1. Nakano, T., Okiyama, Y,, Segawa, K., Saito, Y., Mochizuki, Y., Komeiji, Y. (2024). J. Comput. Chem. Jpn. Int. Ed., 10, 2023-0038. Acceleration of Environmental Electrostatic Potential using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD) Simulation.

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  2. Handa, Y., Okuwaki, K., Kawashima, Y., Hatada, R., Mochizuki, Y., Komeiji, Y. , Tanaka, S., Furuishi, T., Yonemochi, E., Honma, T., Fukuzawa, K. (2024). J. Phys. Chem. B, 128, 2249-2265. 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.

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  3. Tanaka, S., Komeiji, Y. (2022). J. Phys. Chem. Res. 4, 1-2. Thermal and quantum fluctuations of harmonic oscillator.

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  4. Okuwaki, K., Akisawa, K., Hatada, R., Mochizuki, Y., Fukuzawa, K., Komeiji, Y., Tanaka, S. (2022) Appl. Phys. Express 15, 017001. Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method.
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  5. Akisawa, K., Hatada, R., Kitahara, S., Tachino, Y., Mochizuki, Y., Komeiji, Y., Tanaka, S. (2021) Jpn. J. Appl. Phys. 60, 090901. Fragment molecular orbital based interaction analyses on complexes between SARS-CoV-2 RBD variants and ACE2.
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  6. Tanaka, S., Tokutomi, S., Hatada, R., Okuwaki, K., Akisawa, Fukuzawa, K., Komeiji, Y., Okiyama, Y., Mochizuki, Y. (2021) J. Phys. Chem. B 125, 6501-6512. Dynamical cooperativity of ligand-residue interactions evaluated with the fragment molecular orbital method.
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  7. Nakamura, J., Maruyama, Y., Tajima, G., Komeiji, Y., Suwa, M., Sato, C. (2021) Int. J. Mol. Sci. 22, 2624. Ca2+-ATPase molecules as a calcium-sensitive memebrane-endoskeleton of sarcoplasmic reticulum.
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  8. Hatada, R., Okuwaki, K., Akisawa, K., Mochizuki, Y., Handa, Y., Fukuzawa, K., Komeiji, Y., Okiyama, Y., Tanaka, S. (2021) Appl. Phys. Express 14, 027003. Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation.
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  9. Akisawa, K., Hatada, R., Okuwaki, K., Mochizuki, Y., Fukuzawa, K., Komeiji, Y., Tanaka, S. (2021). RSC Adv.11, 3272-3279. Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations.
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  10. Okiyama, Y., Nakano, T., Watanabe, C., Fukuzawa, K., Komeiji, Y., Segawa, K., Mochizuki, Y. (2021) Bull. Chem. Soc. Jpn., 94, 91-96. Acceleration of environmental electrostatic potential using Cholesky decomposition with adaptive metric (CDAM) for fragment molecular orbital (FMO) method.
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  11. Hatada, R., Okuwaki, K., Mochizuki, Y., Handa, Y., Fukuzawa, K., Komeiji, Y., Okiyama,Y., Tanaka S. (2020) J. Chem. Inf. Model. 60, 3593-3602. Fragment molecular orbital based interaction analyses on COVID-19 main protease - inhibitor N3 complex (PDB ID:6LU7).
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  12. Ninomiya, M., Doi, H., Matsumoto, Y., Mochizuki, Y., Komeiji, Y. (2020) Bull. Chem. Soc. Jpn. 93, 553-560. Ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) simulations of (NH3)32 cluster: effects of electron correlation.
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  13. Drobot, B., Schmidt, M., Mochizuki, Y., Abe, T., Okuwaki, K., Brulfert, F., Falke, S., Samsonov, S., Komeiji, Y., Betzel, C., Stumpf, T., Raff, J., Tsushima, S. (2019) Phys. Chem. Chem. Phys. 21, 21213-21222. Cm3+/Eu3+ Induced Structural, Mechanistic and Functional Implications for Calmodulin.
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  14. Hanyu, Y., Komeiji, Y., Kato, M. (2019) Molecules 24, 2949-2959. Potentiating Antigen-Specific Antibody Production with Peptides Obtained from In Silico Screening for High-Affinity Against MHC-II.
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  15. Komeiji, Y., Okiyama, Y., Mochizuki, Y., Fukuzawa, K.(2018) Bull. Chem. Soc. Jpn. 91, 1596-1605. Interaction between a single-stranded DNA and a binding protein viewed by the fragment molecular orbital method.
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  16. Nakano, T., Fukuzawa, K., Okiyama, Y., Watanabe, C., Komeiji, Y., Mochizuki, Y. (2018) CBI J. 18, 119-122. Accuracy of Dimer-ES Approximation on Fragment Molecular Orbital (FMO) Method.
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  17. Saitou, S., Iijima, J., Fujimoto, M., Mochizuki, Y., Okuwaki, K., Doi, H., Komeiji, Y. (2018) CBI J. 18, 58-69. Application of TensorFlow to recognition of visualized results of fragment molecular orbital (FMO) calculations.
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  18. Komeiji, Y., Okiyama Y., Mochizuki, Y., Fukuzawa, K. (2017) CBI J. 17, 72-84. Explicit solvation of a single-stranded DNA, a binding protein, and their complex: a suitable protocol for fragment molecular orbital calculation.
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  19. Yamada, H, Mochizuki, Y., Fukuzawa, K., Okiyama Y., Komeiji, Y. (2017) Comput. Theor. Chem. 1101, 46-54. Fragment molecular orbital (FMO) calculations on DNA by a scaled third-order Moller-Plesset perturbation (MP2.5) scheme.
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  20. Tokuda, K., Watanabe, C., Okiyama, Y., Mochizuki, Y., Fukuzawa, K., Komeiji, Y. (2016) J. Mol. Graph. Model. 69, 144-153. Hydration of Ligands of Influenza Virus Neuraminidase Studied by the Fragment Molecular Orbital Method.
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  21. Fujiwara, T., Mori, H., Komeiji, Y., Mochizuki, Y. (2015) In "Proceedings of Computational Science Workshop 2014 (Tsuchida, E. ed.)", JPS Conf. Proc. 5, 011001. Fragment molecular orbital-based molecular dynamics study on hydrated Ln(III) ions.
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  22. Fukuzawa, K., Kurisaki, I., Watanabe, C., Okiyama, Y., Mochizuki, Y., Tanaka, S., Komeiji, Y. (2015) Comput. Theor. Chem. 1054, 29-37. Explicit solvation modulates intra- and inter-molecular interactions within DNA: electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method.
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  23. Kato, Y., Fujiwara, T., Komeiji, Y., Nakano, T., Mori, H., Okiyama, Y., Mochizuki, Y. (2014) CBI J. 14, 1-13. Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Cu(II) ion.
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  24. Tanaka, S., Mochizuki, Y., Komeiji, Y., Okiyama, Y., Fukuzawa, K. (2014) Phys. Chem. Chem. Phys. 16, 10310-10344. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.
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  25. Fukuzawa, K., Watanabe, C., Kurisaki, I., Taguchi, N., Mochizuki, Y., Nakano, T., Tanaka, S., Komeiji, Y. (2014) Comput. Theor. Chem. 1034, 7-16. Accuracy of the fragment molecular orbital (FMO) calculations for DNA: Total energy, molecular orbital, and inter-fragment interaction energy.
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  26. Komeiji, Y., Fujiwara, T., Okiyama, Y., Mochizuki, Y. (2013) CBI J. 13, 45-57. Dynamic fragmentation with static fragments (DF/SF) algorithm designed for ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) simulations of polypeptides.
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  27. Sato, M., Yamataka, H., Komeiji, Y., Mochizuki, Y. (2012) Chem. Eur. J., 18, 9714-9721. FMO-MD Simulations on Hydration of Formaldehyde in Water Solution with Constraint Dynamics.
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  28. Mori, H., Hirayama, N., Komeiji, Y., Mochizuki, Y. (2012) Comput. Theor. Chem. 986, 30-34. Differences in hydration between cis- and trans-platin: Quantum insights by ab initio fragment molecular orbital-based molecular dynamics (FMO-MD).
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  29. Mochizuki, Y., Nakano, T., Komeiji, Y., Yamashita, K., Okiyama, Y., Yoshikawa, H., Yamataka, H. (2011) Chem. Phys. Lett. 504, 95-99. Fragment molecular orbital-based molecular dynamics (FMO-MD) method with MP2 gradient.
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  30. Sato, M., Yamataka, H., Komeiji, Y., Nakano, T., Mochizuki, Y. (2010) Chem. Eur. J. 16, 6430-6433. Does Amination of Formaldehyde Proceeds through Zwitterionic Intermediate in Water? FMO-MD Simulations by using Constraint Dynamics.
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  31. Fujiwara, T., Mochizuki, Y., Komeiji, Y., Okiyama, Y., Mori, H., Nakano, T., Miyoshi, E. (2010) Chem. Phys. Lett. 490, 41-45. Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Zn(II) ion.
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  32. Komeiji, Y., Mochizuki, Y., Nakano, T. (2010) Chem. Phys. Lett. 484, 380-386. Three-body expansion and generalized dynamic fragmentation improve the Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD).
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  33. Komeiji, Y., Mochizuki, Y., Nakano, T., Fedorov, D. G. (2009) J. Mol. Struct.: THEOCHEM 898, 2-7. Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD), a quantum simulation tool for large molecular systems.
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  34. Komeiji, Y., Ishikawa, T., Mochizuki, Y., Yamataka, H., Nakano, T. (2009) J. Comput. Chem. 30, 40-50. Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation.
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  35. VanSchouwen, B. M. B., Gordon, H. L., Rothstein, S. M., Komeiji, Y., Fukuzawa, K., Tanaka, S. Nakano, T. (2008) Comput. Biol. Chem. 32, 149-158. Water-Mediated Interactions in the CRP-cAMP-DNA Complex: Does water mediate sequence-specific binding at the DNA primary-kink site?
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  36. Sato, M., Yamataka, H., Komeiji, Y., Mochizuki, Y., Ishikawa, T., Nakano, T. (2008) J. Am. Chem. Soc., 130, 2396-2397. How does an SN2 reaction take place in solution? Full Ab initio MD simulations for the hydrolysis of the methyl diazonium ion.
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  37. Komeiji, Y., Ishikawa, T., Mochizuki, Y., Yamataka, H., Nakano, T. (2007) In "Computation in Modern Science and Engineering Vol. 2, Part B - Proc. ICCMSE2007 (Simos, T. E, Maroulis, G., eds, AIP)," pp. 1261-1264. Ab initio FMO-MD method reimplemented and applied to pure water.

  38. Komeiji, Y. (2007) CBI J. 7, 12-23. Implementation of the blue moon ensemble method.
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  39. Kurisaki, I., Fukuzawa, K., Komeiji, Y., Mochizuki, Y., Nakano, T., Imada, J., Chmielewski, A., Rothstein, S. M., Watanabe, H., Tanaka, S. (2007) Biophys. Chem. 130, 1-9. Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method.
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  40. Komeiji, Y., Ishida, T., Fedorov, D. G., Kitaura, K. (2007) J. Comput. Chem. 28, 1750-1762. Change in a protein's electronic structure induced by an explicit solvent: an ab initio Fragment Molecular Orbital (FMO) study of ubiquitin.
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  41. Mochizuki, Y., Komeiji, Y., Ishikawa, T., Nakano, T., Yamataka, H. (2007) Chem. Phys. Lett. 437, 66-72. A fully quantum mechanical simulation study on the lowest n-pi* state of hydrated formaldehyde.
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  42. Ishikawa, T., Mochizuki, Y., Nakano, T., Amari, S., Mori, H., Honda, H., Fujita, T., Tokiwa, H., Tanaka, S., Komeiji, Y., Fukuzawa, K., Tanaka, K., Miyoshi, E. (2006) Chem. Phys. Lett. 427, 159-165. Fragment molecular orbital calculations on large scale systems containing heavy metal atoms.
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  43. Fukuzawa, K., Komeiji, Y., Mochizuki, Y., Kato, A., Nakano, T., Tanaka, S. (2006) J. Comput. Chem., 28, 948-960. Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study.
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    [errata]

  44. Nemoto, T., Fedorov, D. G., Uebayasi, M., Kanazawa, K., Kitaura, K., Komeiji, Y. (2005) Comput. Biol. Chem., 29, 434-439. Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding protein.
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  45. Komeiji, Y., Inadomi, Y., Nakano, T. (2004) Comput. Biol. Chem., 28, 155-161. PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules.
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  46. Komeiji, Y., Nakano, T., Fukuzawa, K., Ueno, Y., Inadomi, Y., Nemoto, T., Uebayasi, M., Fedorov, D. G., Kitaura, K. (2003) Chem. Phys. Lett. 372, 342-347. Fragment molecular orbital method: application to molecular dynamics simulation, "ab initio FMO-MD."
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  47. Komeiji, Y., Uebayasi, M. (2002) CBI J. 2, 102-118. Peach-Grape system - a high performance simulator for biomolecules.
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  48. Komeiji, Y., Ueno, Y., Uebayasi, M. (2002) FEBS Lett., 521, 133-139. Molecular dynamics simulations revealed Ca2+-dependent conformational change of Calmodulin.
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  49. Nemoto, T., Uebayasi, M., Komeiji, Y. (2002) CBI J. 2, 32-37. Flexibility of a loop in a pheromone binding protein from Bombyx mori: a molecular dynamics simulation.
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  50. Komeiji, Y., Haraguchi, M., Nagashima, U. (2001) Parallel Computing 27, 977-987. Parallel molecular dynamics simulation of a protein.
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  51. Kitaura, K., Sugiki, S., Nakano, T., Komeiji, Y., Uebayasi, M., (2001) Chem. Phys. Lett. 336, 163-170. Fragment molecular orbital method: analytical energy gradients.
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  52. Komeiji, Y. (2001) In "Proceedings of Sixth International Symposium on Artificial Life and Robotics (AROB 6th'01)," pp. 349-352. Interaction mechanism between DNA and substrate clarified based on molecular dynamics.

  53. Komeiji, Y. (2000) J. Mol. Struct.: THEOCHEM, 530, 237-243. Ewald summation and multiple time step methods for molecular dynamics simulation of biological molecules.
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  54. Suenaga, A., Yatsu, C., Komeiji, Y., Uebayasi, M., Meguro, T., Yamato, I. (2000) J. Mol. Struct. 526, 209-218. Molecular dynamics simulation of trp-repressor/operator complex: analysis of hydrogen bond patterns of protein-DNA interaction.
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  55. Komeiji, Y., Harata, K., Ueno, Y., Uebayasi, M. (2000) JCPE J. 12, 39-48. Anisotropic motion within a protein: comparison between X-ray crystallography and molecular dynamics simulation of Human Lysozyme.
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  56. Komeiji, Y., Uebayasi, M. (1999) Biophys. J. 77, 123-138. Change in conformation by DNA-peptide association: Molecular dynamics of the Hin-recombinase-hixL complex.
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  57. Komeiji, Y., Uebayasi, M. (1999) Mol. Simul. 21, 303-324. Molecular Dynamics Simulation of the Hin-Recombinase-DNA Complex.
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  58. Suenaga, A., Komeiji, Y., Uebayasi, M., Meguro, T., Saito, M., Yamato, I. (1998) Biosci. Rep. 18, 39-48. Computational observation of an ion permeation through a channel protein.
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  59. Suenaga, A., Komeiji, Y., Uebayasi, M., Meguro, T., Yamato, I. (1998) J. Chem. Software 4, 127-142. Molecular dynamics simulation of unfolding of histidine-containing phosphocarrier protein in water.
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  60. Komeiji, Y., Uebayasi, M., Takata, R., Shimizu, A., Itsukashi, K, Taiji, M. (1997) J. Comput. Chem. 18, 1546-1563. Fast and accurate molecular dynamics simulation of a protein using a special purpose computer.
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  61. Honda, N., Komeiji, Y., Uebayasi, M., Yamato, I. (1996) Proteins 26, 459-464. Computational design of a substrate specificity mutant of a protein.
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  62. Komeiji, Y., Yokoyama, H., Uebayasi, M. Taiji, M. Fukushige, T., Sugimoto, D., Takata, R., Shimizu, A., Itsukashi, K. (1996) In "Pacific Symposium on Biocomputing '96 (Hunter & Klein eds., World Scientific)," pp. 472-487. A High performance system for molecular dynamics simulation of biomolecules using a special-purpose computer.
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  63. Fujita, I., Komeiji, Y., Yamato, I. (1995) Protein Engng. 8, 935-938. Threonine 81 of the trp-repressor of E. coli plays an auxiliary role for the formation of the corepressor binding pocket.
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  64. Komeiji, Y., Uebayasi, M., Yamato, I. (1994) Proteins 30, 248-258. Molecular dynamics simulations of the trp apo- and holo-repressors: domain structure and ligand-protein interaction.
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  65. Komeiji, Y., Fujita, I., Honda, N., Tsutsui, M., Tamura, T., Yamato, I. (1994) Protein Engng.7, 1239-1247. Glycine-85 of the trp-Repressor of E. coli is important in forming the hydrophobic tryptophan binding pocket.
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  66. Komeiji, Y., Honda, N., Yamato, I. (1993) Biophys. Chem. 47, 113-121. Helix propensity of Ala and Val: A free energy perturbation study.
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  67. Komeiji, Y., Uebayasi, M. Someya, J., Yamato, I. (1993) Proteins 16, 268-277. A molecular dynamics study of solvent behavior around a protein.
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  68. Komeiji, Y., Uebayasi, M. Someya, J., Yamato, I. (1992) Protein Engng. 5, 759-767. Free energy perturbation study on a Trp-binding mutant (Ser88->Cys) of the trp-repressor.
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  69. Komeiji, Y., Uebayasi, M. Someya, J., Yamato, I. (1991) Protein Engng. 4, 871-875. Molecular dynamics simulation of trp-aporepressor in a solvent.
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  70. Komeiji, Y., Hanada, K., Yamato, I., Anraku, Y. (1989) FEBS Lett. 256, 135-138. Orientation of the carboxyl terminus of the Na+/proline symport carrier in Escherichia coli.
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Miscellaneous

  1. Maruyama, T., Shimane, Y., Iwasawa, M., Hatada, Y., Yoshida, T., Takaki, Y., Ohishi, K., Tanaka, S., Watanabe H., Xu F., Mochizuki, Y., Fukuzawa, K. Komeiji, Y. (2017) in "Annual report of the Earth simulator center April 2015 - March 2016" pp.255-257. Analysis of Biological Interaction by Fragment Molecular Orbital (FMO) Method - Analyses of the interactions between meals virus hemagglutinins and their receptors -.

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  2. Tsushima, S., Komeiji, Y., Mochizuki, Y. (2017) in "Annual Report 2016 Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf " p. 48. Fragment molecular orbital method for studying lanthanide interactions with proteins.

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  3. Maruyama, T., Shimane, Y., Ohishi, K., Iwasawa, M., Hatada, Y., Takaki, Y., Yoshida, T., Tanaka, S., Anzaki, S., Komeiji, Y., Mochizuki, Y., Fukuzawa, K. (2015) in "Annual report of the Earth simulator center April 2014 - March 2015" pp.131-136. Analysis of Global Ecosystem Ecology by Fragment Molecular Orbital (FMO) Method - Analyses of the interactions between virus hemagglutinins and their receptors -.

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  4. Maruyama, T., Shimane, Y., Ohishi, K., Iwasawa, M., Hatada, Y., Usui, K., Takaki, Y., Yoshida, T., Tanaka, S., Anzaki, S., Komeiji, Y., Watanabe, C., Okiyama, Y., Mochizuki, Y., Fukuzawa, K. (2014) in "Annual report of the Earth simulator center April 2013 - March 2014" pp.155-160. Analysis of Global Ecosystem Ecology by Fragment Molecular Orbital (FMO) Method - Analyses of the interactions between virus hemagglutinins and their receptors -.

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