메뉴 건너뛰기




Volumn 126, Issue 2, 2007, Pages

Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: A general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; ELECTRONIC STRUCTURE; FREE ENERGY; QUANTUM THEORY;

EID: 33846202056     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2424700     Document Type: Article
Times cited : (83)

References (59)
  • 1
    • 85080798568 scopus 로고
    • U. H. Hansmann and Y. Okamoto, Annu. Rev. Comput. Phys. 6, 121 (1989); B. J. Berne and J. E. Straub, Curr. Opin. Struct. Biol. 0959-440X 10.1016/S0959-440X(97)80023-1 7, 181 (1997); T. Schlick, E. Barth, and M. Mandziuk, Annu. Rev. Biophys. Biomol. Struct. 1056-8700 10.1146/annurev.biophys. 26.1.181 26, 181 (1997); D. J. Wales and H. A. Scheraga, Science 0036-8075 10.1126/science.285.5432.1368 285, 1368 (1999); K. Tai, Biophys. Chem. 0301-4622 10.1016/j.bpc.2003.09.010 107, 213 (2004); Y. Okamoto, J. Mol. Graphics Modell. 1093-3263 10.1016/j.jmgm.2003.12.009 22, 424 (2004); R. Elber, Curr. Opin. Struct. Biol. 15, 151 (2005).
    • (1989) , pp. 121
    • Hansmann, U.H.1    Okamoto, Y.2
  • 2
    • 0030904524 scopus 로고    scopus 로고
    • 0959-440X 10.1016/S0959-440X(97)80023-1
    • U. H. Hansmann and Y. Okamoto, Annu. Rev. Comput. Phys. 6, 121 (1989); B. J. Berne and J. E. Straub, Curr. Opin. Struct. Biol. 0959-440X 10.1016/S0959-440X(97)80023-1 7, 181 (1997); T. Schlick, E. Barth, and M. Mandziuk, Annu. Rev. Biophys. Biomol. Struct. 1056-8700 10.1146/annurev.biophys. 26.1.181 26, 181 (1997); D. J. Wales and H. A. Scheraga, Science 0036-8075 10.1126/science.285.5432.1368 285, 1368 (1999); K. Tai, Biophys. Chem. 0301-4622 10.1016/j.bpc.2003.09.010 107, 213 (2004); Y. Okamoto, J. Mol. Graphics Modell. 1093-3263 10.1016/j.jmgm.2003.12.009 22, 424 (2004); R. Elber, Curr. Opin. Struct. Biol. 15, 151 (2005).
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 181
    • Berne, B.J.1    Straub, J.E.2
  • 3
    • 0030918284 scopus 로고    scopus 로고
    • 1056-8700 10.1146/annurev.biophys.26.1.181
    • U. H. Hansmann and Y. Okamoto, Annu. Rev. Comput. Phys. 6, 121 (1989); B. J. Berne and J. E. Straub, Curr. Opin. Struct. Biol. 0959-440X 10.1016/S0959-440X(97)80023-1 7, 181 (1997); T. Schlick, E. Barth, and M. Mandziuk, Annu. Rev. Biophys. Biomol. Struct. 1056-8700 10.1146/annurev.biophys. 26.1.181 26, 181 (1997); D. J. Wales and H. A. Scheraga, Science 0036-8075 10.1126/science.285.5432.1368 285, 1368 (1999); K. Tai, Biophys. Chem. 0301-4622 10.1016/j.bpc.2003.09.010 107, 213 (2004); Y. Okamoto, J. Mol. Graphics Modell. 1093-3263 10.1016/j.jmgm.2003.12.009 22, 424 (2004); R. Elber, Curr. Opin. Struct. Biol. 15, 151 (2005).
    • (1997) Annu. Rev. Biophys. Biomol. Struct. , vol.26 , pp. 181
    • Schlick, T.1    Barth, E.2    Mandziuk, M.3
  • 4
    • 0033610078 scopus 로고    scopus 로고
    • 0036-8075 10.1126/science.285.5432.1368
    • U. H. Hansmann and Y. Okamoto, Annu. Rev. Comput. Phys. 6, 121 (1989); B. J. Berne and J. E. Straub, Curr. Opin. Struct. Biol. 0959-440X 10.1016/S0959-440X(97)80023-1 7, 181 (1997); T. Schlick, E. Barth, and M. Mandziuk, Annu. Rev. Biophys. Biomol. Struct. 1056-8700 10.1146/annurev.biophys. 26.1.181 26, 181 (1997); D. J. Wales and H. A. Scheraga, Science 0036-8075 10.1126/science.285.5432.1368 285, 1368 (1999); K. Tai, Biophys. Chem. 0301-4622 10.1016/j.bpc.2003.09.010 107, 213 (2004); Y. Okamoto, J. Mol. Graphics Modell. 1093-3263 10.1016/j.jmgm.2003.12.009 22, 424 (2004); R. Elber, Curr. Opin. Struct. Biol. 15, 151 (2005).
    • (1999) Science , vol.285 , pp. 1368
    • Wales, D.J.1    Scheraga, H.A.2
  • 5
    • 1242338103 scopus 로고    scopus 로고
    • 0301-4622 10.1016/j.bpc.2003.09.010
    • U. H. Hansmann and Y. Okamoto, Annu. Rev. Comput. Phys. 6, 121 (1989); B. J. Berne and J. E. Straub, Curr. Opin. Struct. Biol. 0959-440X 10.1016/S0959-440X(97)80023-1 7, 181 (1997); T. Schlick, E. Barth, and M. Mandziuk, Annu. Rev. Biophys. Biomol. Struct. 1056-8700 10.1146/annurev.biophys. 26.1.181 26, 181 (1997); D. J. Wales and H. A. Scheraga, Science 0036-8075 10.1126/science.285.5432.1368 285, 1368 (1999); K. Tai, Biophys. Chem. 0301-4622 10.1016/j.bpc.2003.09.010 107, 213 (2004); Y. Okamoto, J. Mol. Graphics Modell. 1093-3263 10.1016/j.jmgm.2003.12.009 22, 424 (2004); R. Elber, Curr. Opin. Struct. Biol. 15, 151 (2005).
    • (2004) Biophys. Chem. , vol.107 , pp. 213
    • Tai, K.1
  • 6
    • 1942455272 scopus 로고    scopus 로고
    • 1093-3263 10.1016/j.jmgm.2003.12.009
    • U. H. Hansmann and Y. Okamoto, Annu. Rev. Comput. Phys. 6, 121 (1989); B. J. Berne and J. E. Straub, Curr. Opin. Struct. Biol. 0959-440X 10.1016/S0959-440X(97)80023-1 7, 181 (1997); T. Schlick, E. Barth, and M. Mandziuk, Annu. Rev. Biophys. Biomol. Struct. 1056-8700 10.1146/annurev.biophys. 26.1.181 26, 181 (1997); D. J. Wales and H. A. Scheraga, Science 0036-8075 10.1126/science.285.5432.1368 285, 1368 (1999); K. Tai, Biophys. Chem. 0301-4622 10.1016/j.bpc.2003.09.010 107, 213 (2004); Y. Okamoto, J. Mol. Graphics Modell. 1093-3263 10.1016/j.jmgm.2003.12.009 22, 424 (2004); R. Elber, Curr. Opin. Struct. Biol. 15, 151 (2005).
    • (2004) J. Mol. Graphics Modell. , vol.22 , pp. 424
    • Okamoto, Y.1
  • 7
    • 17044425870 scopus 로고    scopus 로고
    • U. H. Hansmann and Y. Okamoto, Annu. Rev. Comput. Phys. 6, 121 (1989); B. J. Berne and J. E. Straub, Curr. Opin. Struct. Biol. 0959-440X 10.1016/S0959-440X(97)80023-1 7, 181 (1997); T. Schlick, E. Barth, and M. Mandziuk, Annu. Rev. Biophys. Biomol. Struct. 1056-8700 10.1146/annurev.biophys. 26.1.181 26, 181 (1997); D. J. Wales and H. A. Scheraga, Science 0036-8075 10.1126/science.285.5432.1368 285, 1368 (1999); K. Tai, Biophys. Chem. 0301-4622 10.1016/j.bpc.2003.09.010 107, 213 (2004); Y. Okamoto, J. Mol. Graphics Modell. 1093-3263 10.1016/j.jmgm.2003.12.009 22, 424 (2004); R. Elber, Curr. Opin. Struct. Biol. 15, 151 (2005).
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 151
    • Elber, R.1
  • 8
    • 84953648015 scopus 로고
    • 0021-9606 10.1063/1.462133
    • A. P. Lyubartsev, A. A. Martinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys. 0021-9606 10.1063/1.462133 96, 1776 (1992); E. Marinari and G. Parisi, Europhys. Lett. 0295-5075 19, 451 (1992); A. Irback and F. Potthast, J. Chem. Phys. 0021-9606 10.1063/1.469931 103, 10298 (1995); U. H. E. Hansmann and Y. Okamoto, Phys. Rev. E 1063-651X 10.1103/PhysRevE.54.5863 54, 5863 (1996); U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem. 18, 920 (1997); E. Marinari, G. Parisi, and J. J. Ruiz-Lorenzo, in Spin Glasses and Random Fields, edited by, A. P. Young, (World Scientific, Singapore, 1998), pp. 59-98; A. Irback and E. Sandelin, J. Chem. Phys. 110, 12256 (1999).
    • (1992) J. Chem. Phys. , vol.96 , pp. 1776
    • Lyubartsev, A.P.1    Martinovski, A.A.2    Shevkunov, S.V.3    Vorontsov-Velyaminov, P.N.4
  • 9
    • 33644899039 scopus 로고
    • 0295-5075
    • A. P. Lyubartsev, A. A. Martinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys. 0021-9606 10.1063/1.462133 96, 1776 (1992); E. Marinari and G. Parisi, Europhys. Lett. 0295-5075 19, 451 (1992); A. Irback and F. Potthast, J. Chem. Phys. 0021-9606 10.1063/1.469931 103, 10298 (1995); U. H. E. Hansmann and Y. Okamoto, Phys. Rev. E 1063-651X 10.1103/PhysRevE.54.5863 54, 5863 (1996); U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem. 18, 920 (1997); E. Marinari, G. Parisi, and J. J. Ruiz-Lorenzo, in Spin Glasses and Random Fields, edited by, A. P. Young, (World Scientific, Singapore, 1998), pp. 59-98; A. Irback and E. Sandelin, J. Chem. Phys. 110, 12256 (1999).
    • (1992) Europhys. Lett. , vol.19 , pp. 451
    • Marinari, E.1    Parisi, G.2
  • 10
    • 0000773431 scopus 로고
    • 0021-9606 10.1063/1.469931
    • A. P. Lyubartsev, A. A. Martinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys. 0021-9606 10.1063/1.462133 96, 1776 (1992); E. Marinari and G. Parisi, Europhys. Lett. 0295-5075 19, 451 (1992); A. Irback and F. Potthast, J. Chem. Phys. 0021-9606 10.1063/1.469931 103, 10298 (1995); U. H. E. Hansmann and Y. Okamoto, Phys. Rev. E 1063-651X 10.1103/PhysRevE.54.5863 54, 5863 (1996); U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem. 18, 920 (1997); E. Marinari, G. Parisi, and J. J. Ruiz-Lorenzo, in Spin Glasses and Random Fields, edited by, A. P. Young, (World Scientific, Singapore, 1998), pp. 59-98; A. Irback and E. Sandelin, J. Chem. Phys. 110, 12256 (1999).
    • (1995) J. Chem. Phys. , vol.103 , pp. 10298
    • Irback, A.1    Potthast, F.2
  • 11
    • 0000800852 scopus 로고    scopus 로고
    • 1063-651X 10.1103/PhysRevE.54.5863
    • A. P. Lyubartsev, A. A. Martinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys. 0021-9606 10.1063/1.462133 96, 1776 (1992); E. Marinari and G. Parisi, Europhys. Lett. 0295-5075 19, 451 (1992); A. Irback and F. Potthast, J. Chem. Phys. 0021-9606 10.1063/1.469931 103, 10298 (1995); U. H. E. Hansmann and Y. Okamoto, Phys. Rev. E 1063-651X 10.1103/PhysRevE.54.5863 54, 5863 (1996); U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem. 18, 920 (1997); E. Marinari, G. Parisi, and J. J. Ruiz-Lorenzo, in Spin Glasses and Random Fields, edited by, A. P. Young, (World Scientific, Singapore, 1998), pp. 59-98; A. Irback and E. Sandelin, J. Chem. Phys. 110, 12256 (1999).
    • (1996) Phys. Rev. e , vol.54 , pp. 5863
    • Hansmann, U.H.E.1    Okamoto, Y.2
  • 12
    • 0142013225 scopus 로고    scopus 로고
    • A. P. Lyubartsev, A. A. Martinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys. 0021-9606 10.1063/1.462133 96, 1776 (1992); E. Marinari and G. Parisi, Europhys. Lett. 0295-5075 19, 451 (1992); A. Irback and F. Potthast, J. Chem. Phys. 0021-9606 10.1063/1.469931 103, 10298 (1995); U. H. E. Hansmann and Y. Okamoto, Phys. Rev. E 1063-651X 10.1103/PhysRevE.54.5863 54, 5863 (1996); U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem. 18, 920 (1997); E. Marinari, G. Parisi, and J. J. Ruiz-Lorenzo, in Spin Glasses and Random Fields, edited by, A. P. Young, (World Scientific, Singapore, 1998), pp. 59-98; A. Irback and E. Sandelin, J. Chem. Phys. 110, 12256 (1999).
    • (1997) J. Comput. Chem. , vol.18 , pp. 920
    • Hansmann, U.H.E.1    Okamoto, Y.2
  • 13
    • 0003160962 scopus 로고    scopus 로고
    • edited by A. P.Young (World Scientific, Singapore
    • A. P. Lyubartsev, A. A. Martinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys. 0021-9606 10.1063/1.462133 96, 1776 (1992); E. Marinari and G. Parisi, Europhys. Lett. 0295-5075 19, 451 (1992); A. Irback and F. Potthast, J. Chem. Phys. 0021-9606 10.1063/1.469931 103, 10298 (1995); U. H. E. Hansmann and Y. Okamoto, Phys. Rev. E 1063-651X 10.1103/PhysRevE.54.5863 54, 5863 (1996); U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem. 18, 920 (1997); E. Marinari, G. Parisi, and J. J. Ruiz-Lorenzo, in Spin Glasses and Random Fields, edited by, A. P. Young, (World Scientific, Singapore, 1998), pp. 59-98; A. Irback and E. Sandelin, J. Chem. Phys. 110, 12256 (1999).
    • (1998) Spin Glasses and Random Fields , pp. 59-98
    • Marinari, E.1    Parisi, G.2    Ruiz-Lorenzo, J.J.3
  • 14
    • 0000694475 scopus 로고    scopus 로고
    • A. P. Lyubartsev, A. A. Martinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys. 0021-9606 10.1063/1.462133 96, 1776 (1992); E. Marinari and G. Parisi, Europhys. Lett. 0295-5075 19, 451 (1992); A. Irback and F. Potthast, J. Chem. Phys. 0021-9606 10.1063/1.469931 103, 10298 (1995); U. H. E. Hansmann and Y. Okamoto, Phys. Rev. E 1063-651X 10.1103/PhysRevE.54.5863 54, 5863 (1996); U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem. 18, 920 (1997); E. Marinari, G. Parisi, and J. J. Ruiz-Lorenzo, in Spin Glasses and Random Fields, edited by, A. P. Young, (World Scientific, Singapore, 1998), pp. 59-98; A. Irback and E. Sandelin, J. Chem. Phys. 110, 12256 (1999).
    • (1999) J. Chem. Phys. , vol.110 , pp. 12256
    • Irback, A.1    Sandelin, E.2
  • 15
    • 35949020425 scopus 로고
    • 0031-9007 10.1103/PhysRevLett.57.2607
    • R. H. Swendsen and F. S. Wang, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.57.2607 57, 2607 (1986); G. F. Gerer, Stat. Sci. 0883-4237 7, 437 (1992); K. Hukusima and K. Namoto, J. Phys. Soc. Jpn. 0031-9015 10.1143/JPSJ.65.1604 65, 1604 (1996); U. H. Hansmann, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(97)01198-6 281, 140 (1997); Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(99)01123-9 314, 141 (1999); K. Y. Sanbonmatsu and A. E. Garcia, Proteins 46, 225 (2002).
    • (1986) Phys. Rev. Lett. , vol.57 , pp. 2607
    • Swendsen, R.H.1    Wang, F.S.2
  • 16
    • 0000024111 scopus 로고
    • 0883-4237
    • R. H. Swendsen and F. S. Wang, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.57.2607 57, 2607 (1986); G. F. Gerer, Stat. Sci. 0883-4237 7, 437 (1992); K. Hukusima and K. Namoto, J. Phys. Soc. Jpn. 0031-9015 10.1143/JPSJ.65.1604 65, 1604 (1996); U. H. Hansmann, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(97)01198-6 281, 140 (1997); Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(99)01123-9 314, 141 (1999); K. Y. Sanbonmatsu and A. E. Garcia, Proteins 46, 225 (2002).
    • (1992) Stat. Sci. , vol.7 , pp. 437
    • Gerer, G.F.1
  • 17
    • 0030516672 scopus 로고    scopus 로고
    • 0031-9015 10.1143/JPSJ.65.1604
    • R. H. Swendsen and F. S. Wang, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.57.2607 57, 2607 (1986); G. F. Gerer, Stat. Sci. 0883-4237 7, 437 (1992); K. Hukusima and K. Namoto, J. Phys. Soc. Jpn. 0031-9015 10.1143/JPSJ.65.1604 65, 1604 (1996); U. H. Hansmann, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(97)01198-6 281, 140 (1997); Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(99)01123-9 314, 141 (1999); K. Y. Sanbonmatsu and A. E. Garcia, Proteins 46, 225 (2002).
    • (1996) J. Phys. Soc. Jpn. , vol.65 , pp. 1604
    • Hukusima, K.1    Namoto, K.2
  • 18
    • 0031578972 scopus 로고    scopus 로고
    • 0009-2614 10.1016/S0009-2614(97)01198-6
    • R. H. Swendsen and F. S. Wang, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.57.2607 57, 2607 (1986); G. F. Gerer, Stat. Sci. 0883-4237 7, 437 (1992); K. Hukusima and K. Namoto, J. Phys. Soc. Jpn. 0031-9015 10.1143/JPSJ.65.1604 65, 1604 (1996); U. H. Hansmann, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(97)01198-6 281, 140 (1997); Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(99)01123-9 314, 141 (1999); K. Y. Sanbonmatsu and A. E. Garcia, Proteins 46, 225 (2002).
    • (1997) Chem. Phys. Lett. , vol.281 , pp. 140
    • Hansmann, U.H.1
  • 19
    • 0001616080 scopus 로고    scopus 로고
    • 0009-2614 10.1016/S0009-2614(99)01123-9
    • R. H. Swendsen and F. S. Wang, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.57.2607 57, 2607 (1986); G. F. Gerer, Stat. Sci. 0883-4237 7, 437 (1992); K. Hukusima and K. Namoto, J. Phys. Soc. Jpn. 0031-9015 10.1143/JPSJ.65.1604 65, 1604 (1996); U. H. Hansmann, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(97)01198-6 281, 140 (1997); Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(99)01123-9 314, 141 (1999); K. Y. Sanbonmatsu and A. E. Garcia, Proteins 46, 225 (2002).
    • (1999) Chem. Phys. Lett. , vol.314 , pp. 141
    • Sugita, Y.1    Okamoto, Y.2
  • 20
    • 0036467163 scopus 로고    scopus 로고
    • R. H. Swendsen and F. S. Wang, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.57.2607 57, 2607 (1986); G. F. Gerer, Stat. Sci. 0883-4237 7, 437 (1992); K. Hukusima and K. Namoto, J. Phys. Soc. Jpn. 0031-9015 10.1143/JPSJ.65.1604 65, 1604 (1996); U. H. Hansmann, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(97)01198-6 281, 140 (1997); Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(99)01123-9 314, 141 (1999); K. Y. Sanbonmatsu and A. E. Garcia, Proteins 46, 225 (2002).
    • (2002) Proteins , vol.46 , pp. 225
    • Sanbonmatsu, K.Y.1    Garcia, A.E.2
  • 24
    • 0036286654 scopus 로고    scopus 로고
    • 0001-4842 10.1021/ar010030m
    • T. Simonson, G. Archontis, and M. Karplus, Acc. Chem. Res. 0001-4842 10.1021/ar010030m 35, 430 (2002); P. Kollman, Chem. Rev. (Washington, D.C.) 93, 2395 (1993).
    • (2002) Acc. Chem. Res. , vol.35 , pp. 430
    • Simonson, T.1    Archontis, G.2    Karplus, M.3
  • 25
    • 7044239742 scopus 로고
    • T. Simonson, G. Archontis, and M. Karplus, Acc. Chem. Res. 0001-4842 10.1021/ar010030m 35, 430 (2002); P. Kollman, Chem. Rev. (Washington, D.C.) 93, 2395 (1993).
    • (1993) Chem. Rev. (Washington, D.C.) , vol.93 , pp. 2395
    • Kollman, P.1
  • 26
    • 0034743155 scopus 로고    scopus 로고
    • 0066-426X 10.1146/annurev.physchem.52.1.499
    • C. L. Brooks and J. E. Shea, Annu. Rev. Phys. Chem. 0066-426X 10.1146/annurev.physchem.52.1.499 52, 499 (2001); C. D. Snow, E. J. Sorin, Y. M. Rhee, and V. S. Pande, Annu. Rev. Biophys. Biomol. Struct. 34, 43 (2005).
    • (2001) Annu. Rev. Phys. Chem. , vol.52 , pp. 499
    • Brooks, C.L.1    Shea, J.E.2
  • 28
    • 0034294024 scopus 로고    scopus 로고
    • 0021-9606 10.1063/1.1308516
    • Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. 0021-9606 10.1063/1.1308516 113, 6042 (2000); H. Fukunishi, O. Watanabe, and S. Takada, J. Chem. Phys. 0021-9606 10.1063/1.1472510 116, 9058 (2002); S. M. Jang, S. Shin, and Y. Pak, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.91.058305 91, 058305 (2003); W. Kwak and U. H. E. Hansmann, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.95.138102 95, 138102 (2005); P. Liu, B. Kim, R. A. Friesner, and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas. 0506346102 102, 13749 (2005); P. Liu, X. Huang, R. Zhou, and B. J. Berne, J. Phys. Chem. B 110, 19018 (2006).
    • (2000) J. Chem. Phys. , vol.113 , pp. 6042
    • Sugita, Y.1    Kitao, A.2    Okamoto, Y.3
  • 29
    • 0037157317 scopus 로고    scopus 로고
    • 0021-9606 10.1063/1.1472510
    • Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. 0021-9606 10.1063/1.1308516 113, 6042 (2000); H. Fukunishi, O. Watanabe, and S. Takada, J. Chem. Phys. 0021-9606 10.1063/1.1472510 116, 9058 (2002); S. M. Jang, S. Shin, and Y. Pak, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.91.058305 91, 058305 (2003); W. Kwak and U. H. E. Hansmann, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.95.138102 95, 138102 (2005); P. Liu, B. Kim, R. A. Friesner, and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas. 0506346102 102, 13749 (2005); P. Liu, X. Huang, R. Zhou, and B. J. Berne, J. Phys. Chem. B 110, 19018 (2006).
    • (2002) J. Chem. Phys. , vol.116 , pp. 9058
    • Fukunishi, H.1    Watanabe, O.2    Takada, S.3
  • 30
    • 0141976331 scopus 로고    scopus 로고
    • 0031-9007 10.1103/PhysRevLett.91.058305
    • Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. 0021-9606 10.1063/1.1308516 113, 6042 (2000); H. Fukunishi, O. Watanabe, and S. Takada, J. Chem. Phys. 0021-9606 10.1063/1.1472510 116, 9058 (2002); S. M. Jang, S. Shin, and Y. Pak, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.91.058305 91, 058305 (2003); W. Kwak and U. H. E. Hansmann, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.95.138102 95, 138102 (2005); P. Liu, B. Kim, R. A. Friesner, and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas. 0506346102 102, 13749 (2005); P. Liu, X. Huang, R. Zhou, and B. J. Berne, J. Phys. Chem. B 110, 19018 (2006).
    • (2003) Phys. Rev. Lett. , vol.91 , pp. 058305
    • Jang, S.M.1    Shin, S.2    Pak, Y.3
  • 31
    • 27144440086 scopus 로고    scopus 로고
    • 0031-9007 10.1103/PhysRevLett.95.138102
    • Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. 0021-9606 10.1063/1.1308516 113, 6042 (2000); H. Fukunishi, O. Watanabe, and S. Takada, J. Chem. Phys. 0021-9606 10.1063/1.1472510 116, 9058 (2002); S. M. Jang, S. Shin, and Y. Pak, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.91.058305 91, 058305 (2003); W. Kwak and U. H. E. Hansmann, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.95.138102 95, 138102 (2005); P. Liu, B. Kim, R. A. Friesner, and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas. 0506346102 102, 13749 (2005); P. Liu, X. Huang, R. Zhou, and B. J. Berne, J. Phys. Chem. B 110, 19018 (2006).
    • (2005) Phys. Rev. Lett. , vol.95 , pp. 138102
    • Kwak, W.1    Hansmann, U.H.E.2
  • 32
    • 25444481354 scopus 로고    scopus 로고
    • 0027-8424 10.1073/pnas.0506346102
    • Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. 0021-9606 10.1063/1.1308516 113, 6042 (2000); H. Fukunishi, O. Watanabe, and S. Takada, J. Chem. Phys. 0021-9606 10.1063/1.1472510 116, 9058 (2002); S. M. Jang, S. Shin, and Y. Pak, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.91.058305 91, 058305 (2003); W. Kwak and U. H. E. Hansmann, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.95.138102 95, 138102 (2005); P. Liu, B. Kim, R. A. Friesner, and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas. 0506346102 102, 13749 (2005); P. Liu, X. Huang, R. Zhou, and B. J. Berne, J. Phys. Chem. B 110, 19018 (2006).
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 13749
    • Liu, P.1    Kim, B.2    Friesner, R.A.3    Berne, B.J.4
  • 33
    • 33749605444 scopus 로고    scopus 로고
    • Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. 0021-9606 10.1063/1.1308516 113, 6042 (2000); H. Fukunishi, O. Watanabe, and S. Takada, J. Chem. Phys. 0021-9606 10.1063/1.1472510 116, 9058 (2002); S. M. Jang, S. Shin, and Y. Pak, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.91.058305 91, 058305 (2003); W. Kwak and U. H. E. Hansmann, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.95.138102 95, 138102 (2005); P. Liu, B. Kim, R. A. Friesner, and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas. 0506346102 102, 13749 (2005); P. Liu, X. Huang, R. Zhou, and B. J. Berne, J. Phys. Chem. B 110, 19018 (2006).
    • (2006) J. Phys. Chem. B , vol.110 , pp. 19018
    • Liu, P.1    Huang, X.2    Zhou, R.3    Berne, B.J.4
  • 34
    • 36449006131 scopus 로고
    • 0021-9606 10.1063/1.461157
    • A. Roitberg and R. Elber, J. Chem. Phys. 0021-9606 10.1063/1.461157 95, 9277 (1991); C. Simmerling and R. Elber, J. Am. Chem. Soc. 116, 2534 (1994).
    • (1991) J. Chem. Phys. , vol.95 , pp. 9277
    • Roitberg, A.1    Elber, R.2
  • 35
    • 0028150192 scopus 로고
    • A. Roitberg and R. Elber, J. Chem. Phys. 0021-9606 10.1063/1.461157 95, 9277 (1991); C. Simmerling and R. Elber, J. Am. Chem. Soc. 116, 2534 (1994).
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 2534
    • Simmerling, C.1    Elber, R.2
  • 40
    • 0034226506 scopus 로고    scopus 로고
    • 1089-5647 10.1021/jp001177i
    • S. Banba, Z. Y. Guo, and C. L. Brooks III, J. Phys. Chem. B 1089-5647 10.1021/jp001177i 104, 6903 (2000); K. Damodaran, S. Banba, and C. L. Brooks III, J. Phys. Chem. B 105, 9316 (2001).
    • (2000) J. Phys. Chem. B , vol.104 , pp. 6903
    • Banba, S.1    Guo, Z.Y.2    Brooks Iii, C.L.3
  • 41
    • 0035960174 scopus 로고    scopus 로고
    • S. Banba, Z. Y. Guo, and C. L. Brooks III, J. Phys. Chem. B 1089-5647 10.1021/jp001177i 104, 6903 (2000); K. Damodaran, S. Banba, and C. L. Brooks III, J. Phys. Chem. B 105, 9316 (2001).
    • (2001) J. Phys. Chem. B , vol.105 , pp. 9316
    • Damodaran, K.1    Banba, S.2    Brooks Iii, C.L.3
  • 42
    • 0033545623 scopus 로고    scopus 로고
    • 0022-2623 10.1021/jm980277y
    • M. A. Eriksson, J. Pitera, and P. A. Kollman, J. Med. Chem. 0022-2623 10.1021/jm980277y 42, 868 (1999); J. W. Pitera and P. A. Kollman, Proteins: Struct., Funct., Genet. 41, 385 (2000).
    • (1999) J. Med. Chem. , vol.42 , pp. 868
    • Eriksson, M.A.1    Pitera, J.2    Kollman, P.A.3
  • 44
    • 84986513644 scopus 로고
    • 0192-8651 10.1002/jcc.540110605
    • M. J. Field, P. A. Bash, and M. Karplus, J. Comput. Chem. 0192-8651 10.1002/jcc.540110605 11, 700 (1990); A. Warshel, Annu. Rev. Biophys. Biomol. Struct. 32, 425 (2003).
    • (1990) J. Comput. Chem. , vol.11 , pp. 700
    • Field, M.J.1    Bash, P.A.2    Karplus, M.3
  • 45
    • 0041876227 scopus 로고    scopus 로고
    • M. J. Field, P. A. Bash, and M. Karplus, J. Comput. Chem. 0192-8651 10.1002/jcc.540110605 11, 700 (1990); A. Warshel, Annu. Rev. Biophys. Biomol. Struct. 32, 425 (2003).
    • (2003) Annu. Rev. Biophys. Biomol. Struct. , vol.32 , pp. 425
    • Warshel, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.