참고문헌
- Amari, S. Aizawa, M., Zhang, J., Fukuzawa, K., Mochizuki, Y., Iwasawa, Y., Nakata, K., Chuman, H. and Nakano T., VISCANA: Visualized Cluster Analysis of Protein-Ligand Interaction Based onthe ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening, J. Chem. Inf. Comput. Sci. 46 (2006) 221-230. https://doi.org/10.1021/ci050262q
- Fedorov, D. G, Kitaura, K., Li, H., Jensen, J. H. and Gordon, M. S. (2006) The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO), J. Comp. Chem. 27 976-985. https://doi.org/10.1002/jcc.20406
- Fischer, B., Fukuzawa, K. and Wenzel, W. (2008) Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery, Proteins: Struct., Funct., Bioinf. 70 1264-1273. https://doi.org/10.1002/prot.21607
- Fukuzawa, K., Kitaura, K., Uebayasi, M., Nakata, N., Kaminuma T. and Nakano, T. (2005) Ab initio quantum mechanical study of the binding energies of human estrogen receptor with its ligands: An application of fragment molecular orbital method, J. Comput. Chem. 26 1-10. https://doi.org/10.1002/jcc.20130
- Fukuzawa, K., Mochizuki, Y., Tanaka, S., Kitaura, K., Nakano, T. (2006) Molecular Interactions between Estrogen Receptor and Its Ligand Studied by the ab Initio Fragment Molecular Orbital Method, J. Phys. Chem. B 110 16102-16110. https://doi.org/10.1021/jp060770i
- Fujitani, H., Tanida, Y., Matsuura, A. (2009) Massively parallel computation of absolute binding free energy with well-equilibrated states, Phys. Rev. E 79 021914. https://doi.org/10.1103/PhysRevE.79.021914
- Harada, T., Yamagishi, K., Nakano, N., Kitaura, K. and Tokiwa, H. (2008) Ab initio fragment molecular orbital study of ligand binding to human progesterone receptor ligand-binding domain, Naunyn-Schmiedeberg's Arch. Pharmac. 377 607-615.
- Ishikawa, T., Mochizuki, Y., Nakano, T., Amari, S., Mori, H., Honda, H., Fujita, T., Tokiwa, H., Tanaka, S., Komeiji, Y., Fukuzawa, K., Tanaka, K. and Miyoshi, E. (2006) Fragment molecular orbital calculations on large scale systems containing heavy metal atom, Chem. Phys. Lett. 427 159-165. https://doi.org/10.1016/j.cplett.2006.06.103
- Ishikawa, T., Mochizuki, Y., Amari, S., Nakano, T., Tokiwa, H., Tanaka, S. and Tanaka, K. (2007) Fragment interaction analysis based on local MP2, Theor. Chem. Acc. 118 937-945. https://doi.org/10.1007/s00214-007-0374-7
- Ishikawa, T., Mochizuki, Y., Amari, S., Nakano, T., Tanaka, S. and Tanaka, K. (2008) An application of fragment interaction analysis based on local MP2, Chem. Phys. Lett. 463 189-194. https://doi.org/10.1016/j.cplett.2008.08.022
- Ito, M., Fukuzawa, K., Mochizuki, Y., Nakano, T. and Tanaka, S. (2007) 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, J. Phys. Chem. B 111 3525-3533. https://doi.org/10.1021/jp070054w
- Ito, M., Fukuzawa, K., Mochizuki, Y., Nakano, T., Tanaka, S. (2008 a) 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, , J. Phys. Chem. A 112 1986-1998. https://doi.org/10.1021/jp075430r
- Ito, M., Fukuzawa, K., Ishikawa, T., Mochizuki, Y., Nakano, T., Tanaka S. (2008 b) Ab Initio Fragment Molecular Orbital Study of Molecular Interactions in Liganded Retinoid X Receptor: Specification of Residues Associated with Ligand Inducible Information Transmission, , J. Phys. Chem. B. 112 (2008) 12081-12094. https://doi.org/10.1021/jp803369x
- Kurisaki, I., Fukuzawa, K., Komeiji, Y., Mochizuki, Y., Nakano, T., Imada, J., Chmielewski, A., Rothstein, S. M., Watanabe, H., Tanaka S. (2007) Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method, Biophys. Chem. 130 1-9. https://doi.org/10.1016/j.bpc.2007.06.011
- Li, H., Fedorov, D.G., Nagata, T., Kitaura, K., Jensen, J. H., Gordon M. S. (2010) Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation. J. Comp. Chem. 31 778-790.
- Mochizuki, M., Koikegami, S., Nakano, T., Amari S. and Kitaura K. (2004a) Large scale MP2 calculations with fragment molecular orbital scheme, Chem. Phys. Lett. 396, 473-479. https://doi.org/10.1016/j.cplett.2004.08.082
- Mochizuki, Y., Nakano, T., Koikegami, S., Tanimori, S., Abe, Y., Nagashima U. and Kitaura K. (2004b) A parallelized integraldirect second-order Moeller-Plesset perturbation theory method with a fragment molecular orbital scheme, Theor. Chem. Acc. 112 442-452. https://doi.org/10.1007/s00214-004-0602-3
- Mochizuki, Y., Fukuzawa, K., Kato, A., Tanaka, S., Kitaura, K. and Nakano, T. (2005) A configuration analysis for fragment interaction, , Chem. Phys. Lett. 410 247-253. https://doi.org/10.1016/j.cplett.2005.05.079
- Mochizuki, Y., Yamashita, K., Murase, T., Nakano, T., Fukuzawa, K., Takematsu, K., Watanabe, H. and Tanaka S. (2008) Large scale FMO-MP2 calculations on a massively parallel-vector computer, Chem. Phys. Lett. 457 396-403. https://doi.org/10.1016/j.cplett.2008.03.090
- Nakano, T., Kaminuma, T., Sato, T., Akiyama, Y., Uebayasi, M. and Kitaura, K. (2000) Fragment molecular orbital method: application to polypeptides. Chem. Phys. Lett. 318 614-618. https://doi.org/10.1016/S0009-2614(00)00070-1
- Nakano, T., Kaminuma, T., Sato, T., Fukuzawa, K., Akiyama, Y., Uebayasi and M., Kitaura, K. (2002) Fragment molecular orbital method: use of approximate electrostatic potential, Chem. Phys. Lett. 351 475-480. https://doi.org/10.1016/S0009-2614(01)01416-6
- Okiyama, Y., Watanabe, H., Fukuzawa, K., Nakano, T., Mochizuki, Y., Ishikawa, T., Tanaka, S., Ebina K. (2007) Application of the fragment molecular orbital method for determination of atomic charges on polypeptides, Chem. Phys. Lett. 449 329-335. https://doi.org/10.1016/j.cplett.2007.10.066
- Okiyama, Y., Watanabe, H., Fukuzawa, K., Nakano, T., Mochizuki, Y., Ishikawa, T., Ebina, K., Tanaka, S. (2009) Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations, Chem. Phys. Lett. 467 417-423. https://doi.org/10.1016/j.cplett.2008.11.044
- Okiyama, Y., Nakano, T., Yamashita, K., Mochizuki, Y., Taguchi, N., Tanaka S. (2010) Acceleration of fragment molecular orbital calculations with Cholesky decomposition approach, Chem. Phys. Lett. 490 84-89. https://doi.org/10.1016/j.cplett.2010.03.001
- Rezac, J., Jurecka, P., Riley, K. E., Cerny, J., Valdes, H., Pluhackova, K., Berka, K.; Rezac, T.; Pitonak, M.; Vondrasek, J.; Hobza, P. (2008) Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples, Collect. Czech. Chem. Commun. 73, 1261-1270. https://doi.org/10.1135/cccc20081261
- Szabo, A. and Ostlund, N. S. (1982) Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory, McGraw-Hill, New York.
- Yamagishi, K., Yamamoto, K. Yamada S., and H. Tokiwa (2006) Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital-interfragment interaction energy analysis, Chem. Phys. Lett. 420 (2006) 465-468. https://doi.org/10.1016/j.cplett.2005.12.078
- Yoda, T., Sugita, Y., Okamoto, Y. (2004) Comparisons of force fields for proteins by generalized-ensemble simulations, Chem. Phys. Lett. 386 460-467. https://doi.org/10.1016/j.cplett.2004.01.078
- Yoshida, T., Yamagishi, K., Chuman, H. (2008) QSAR Study of Cyclic Urea Type HIV-1 PR Inhibitors Using Ab Initio MO Calculation of Their Complex Structures with HIV-1, QSAR Comb. Sci. 27 694-703. https://doi.org/10.1002/qsar.200730108
- Yoshida, T., Fujita, T., Chuman, H., (2009) 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, Curr. Comp.- Aided Drug Des. 5 38-55. https://doi.org/10.2174/157340909787580845
- Watanabe, H., Tanaka, S., Okimoto, N., Hasegawa, A., Taiji. M., Tanida Y., Mitsui T., Katsuyama M., Fujitani, H., (2010) Comparison of binding affinity evaluations for FKBP ligands with state-of-the-art computational methods: FMO, QM/MM, MMPB/SA and MP-CAFEE approaches, Chem-Bio Informatics Journal 10 32-45. https://doi.org/10.1273/cbij.10.32
피인용 문헌
- Use of QM/MM scheme to reproduce macromolecule–small molecule noncovalent binding energy vol.991, 2012, https://doi.org/10.1016/j.comptc.2012.04.010
- Fragment library design considerations vol.2, pp.6, 2012, https://doi.org/10.1002/wcms.1098