SCOPUS 정보 검색 플랫폼

Journal of Chemical Theory and Computation

Volumn 7, Issue 9, 2011, Pages 2721-2727

Computing alchemical free energy differences with Hamiltonian replica exchange molecular dynamics (H-REMD) simulations

(3) Meng, Yilin a Sabri Dashti, Danial b Roitberg, Adrian E b

a UNIVERSITY OF CHICAGO (United States)

b UNIVERSITY OF FLORIDA (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 80052803759 PISSN: 15499618 EISSN: 15499626 Source Type: Journal
DOI: 10.1021/ct200153u Document Type: Article

Times cited : (83)

References (42)

1
- 62849084788
- Eds. Springer Verlag: Berlin
- Free energy calculations. Theory and applications in chemistry and biology; Chipot, C., Pohorille, A., Eds.; Springer Verlag: Berlin, 2007.
- (2007) Free Energy Calculations. Theory and Applications in Chemistry and Biology
- Chipot, C.¹ Pohorille, A.²

2
- 0023106632
- Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A. Science 1987, 235, 574-576
- (1987) Science , vol.235 , pp. 574-576
- Bash, P.A.¹ Singh, U.C.² Brown, F.K.³ Langridge, R.⁴ Kollman, P.A.⁵

3
- 36849122972
- Zwanzig, R. W. J. Chem. Phys. 1954, 22, 1420-1426
- (1954) J. Chem. Phys. , vol.22 , pp. 1420-1426
- Zwanzig, R.W.¹

4
- 33646471468
- Kirkwood, J. G. J. Chem. Phys. 1935, 3, 300-313
- (1935) J. Chem. Phys. , vol.3 , pp. 300-313
- Kirkwood, J.G.¹

5
- 0001626776
- Mezei, M. J. Comput. Phys. 1987, 68, 237-248
- (1987) J. Comput. Phys. , vol.68 , pp. 237-248
- Mezei, M.¹

6
- 0029633155
- Roux, B. Comput. Phys. Commun. 1995, 91, 275-282
- (1995) Comput. Phys. Commun. , vol.91 , pp. 275-282
- Roux, B.¹

7
- 0342929614
- Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187-199
- (1977) J. Comput. Phys. , vol.23 , pp. 187-199
- Torrie, G.M.¹ Valleau, J.P.²

8
- 4243754128
- Jarzynski, C. Phys. Rev. Lett. 1997, 78, 2690-2693
- (1997) Phys. Rev. Lett. , vol.78 , pp. 2690-2693
- Jarzynski, C.¹

9
- 84986519238
- Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021
- (1992) J. Comput. Chem. , vol.13 , pp. 1011-1021
- Kumar, S.¹ Bouzida, D.² Swendsen, R.H.³ Kollman, P.A.⁴ Rosenberg, J.M.⁵

10
- 5244304444
- Bennett, C. H. J. Comput. Phys. 1976, 22, 245-268
- (1976) J. Comput. Phys. , vol.22 , pp. 245-268
- Bennett, C.H.¹

11
- 52949088587
- Shirts, M. R.; Chodera, J. D. J. Chem. Phys. 2008, 129, 124105
- (2008) J. Chem. Phys. , vol.129 , pp. 124105
- Shirts, M.R.¹ Chodera, J.D.²

12
- 77955577540
- Pohorille, A.; Jarzynski, C.; Chipot, C. J. Phys. Chem. B 2010, 114, 10235-10253
- (2010) J. Phys. Chem. B , vol.114 , pp. 10235-10253
- Pohorille, A.¹ Jarzynski, C.² Chipot, C.³

13
- 0346350789
- Woods, C. J.; Essex, J. W.; King, M. A. J. Phys. Chem. B 2003, 107, 13703-13710
- (2003) J. Phys. Chem. B , vol.107 , pp. 13703-13710
- Woods, C.J.¹ Essex, J.W.² King, M.A.³

14
- 58149512801
- Zheng, L. Q.; Chen, M. G.; Yang, W. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 20227-20232
- (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 20227-20232
- Zheng, L.Q.¹ Chen, M.G.² Yang, W.³

15
- 0001616080
- Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 1999, 314, 141-151
- (1999) Chem. Phys. Lett. , vol.314 , pp. 141-151
- Sugita, Y.¹ Okamoto, Y.²

16
- 3142716857
- Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120, 11919-11929
- (2004) J. Chem. Phys. , vol.120 , pp. 11919-11929
- Hamelberg, D.¹ Mongan, J.² McCammon, J.A.³

17
- 0037157317
- Fukunishi, H.; Watanabe, O.; Takada, S. J. Chem. Phys. 2002, 116, 9058-9067
- (2002) J. Chem. Phys. , vol.116 , pp. 9058-9067
- Fukunishi, H.¹ Watanabe, O.² Takada, S.³

18
- 25444481354
- Liu, P.; Kim, B.; Friesner, R. A.; Berne, B. J. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 13749-13754
- (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 13749-13754
- Liu, P.¹ Kim, B.² Friesner, R.A.³ Berne, B.J.⁴

19
- 33847717840
- Liu, P.; Voth, G. A. J. Chem. Phys. 2007, 126, 045106
- (2007) J. Chem. Phys. , vol.126 , pp. 045106
- Liu, P.¹ Voth, G.A.²

20
- 32644458379
- Lyman, E.; Ytreberg, F. M.; Zuckerman, D. M. Phys. Rev. Lett. 2006, 96, 028105
- (2006) Phys. Rev. Lett. , vol.96 , pp. 028105
- Lyman, E.¹ Ytreberg, F.M.² Zuckerman, D.M.³

21
- 33846254959
- Lwin, T. Z.; Luo, R. J. Chem. Phys. 2005, 123, 194904
- (2005) J. Chem. Phys. , vol.123 , pp. 194904
- Lwin, T.Z.¹ Luo, R.²

22
- 0346255348
- Woods, C. J.; Essex, J. W.; King, M. A. J. Phys. Chem. B 2003, 107, 13711-13718
- (2003) J. Phys. Chem. B , vol.107 , pp. 13711-13718
- Woods, C.J.¹ Essex, J.W.² King, M.A.³

23
- 33846264022
- Rick, S. W. J. Chem. Theory Comput. 2006, 2, 939-946
- (2006) J. Chem. Theory Comput. , vol.2 , pp. 939-946
- Rick, S.W.¹

24
- 34247266675
- Min, D. H.; Li, H. Z.; Li, G. H.; Bitetti-Putzer, R.; Yang, W. J. Chem. Phys. 2007, 126, 144109
- (2007) J. Chem. Phys. , vol.126 , pp. 144109
- Min, D.H.¹ Li, H.Z.² Li, G.H.³ Bitetti-Putzer, R.⁴ Yang, W.⁵

25
- 73949121918
- Jiang, W.; Hodoscek, M.; Roux, B. J. Chem. Theory Comput. 2009, 5, 2583-2588
- (2009) J. Chem. Theory Comput. , vol.5 , pp. 2583-2588
- Jiang, W.¹ Hodoscek, M.² Roux, B.³

26
- 77956574437
- Jiang, W.; Roux, B. J. Chem. Theory Comput. 2010, 6, 2559-2565
- (2010) J. Chem. Theory Comput. , vol.6 , pp. 2559-2565
- Jiang, W.¹ Roux, B.²

27
- 0025755942
- Dyson, H. J.; Tennant, L. L.; Holmgren, A. Biochemistry 1991, 30, 4262-4268
- (1991) Biochemistry , vol.30 , pp. 4262-4268
- Dyson, H.J.¹ Tennant, L.L.² Holmgren, A.³

28
- 0025718561
- Langsetmo, K.; Fuchs, J. A.; Woodward, C. Biochemistry 1991, 30, 7603-7609
- (1991) Biochemistry , vol.30 , pp. 7603-7609
- Langsetmo, K.¹ Fuchs, J.A.² Woodward, C.³

29
- 77952390528
- Christ, C. D.; Mark, A. E.; van Gunsteren, W. F. J. Comput. Chem. 2010, 31, 1569-1582
- (2010) J. Comput. Chem. , vol.31 , pp. 1569-1582
- Christ, C.D.¹ Mark, A.E.² Van Gunsteren, W.F.³

30
- 47749107217
- Jorgensen, W. L.; Thomas, L. L. J. Chem. Theory Comput. 2008, 4, 869-876
- (2008) J. Chem. Theory Comput. , vol.4 , pp. 869-876
- Jorgensen, W.L.¹ Thomas, L.L.²

31
- 7044239742
- Kollman, P. Chem. Rev. 1993, 93, 2395-2417
- (1993) Chem. Rev. , vol.93 , pp. 2395-2417
- Kollman, P.¹

32
- 0010234315
- Straatsma, T. P.; Mccammon, J. A. Annu. Rev. Phys. Chem. 1992, 43, 407-435
- (1992) Annu. Rev. Phys. Chem. , vol.43 , pp. 407-435
- Straatsma, T.P.¹ McCammon, J.A.²

33
- 0004504539
- Jorgensen, W. L.; Ravimohan, C. J. Chem. Phys. 1985, 83, 3050-3054
- (1985) J. Chem. Phys. , vol.83 , pp. 3050-3054
- Jorgensen, W.L.¹ Ravimohan, C.²

34
- 0345763766
- Lu, N. D.; Kofke, D. A.; Woolf, T. B. J. Comput. Chem. 2004, 25, 28-39
- (2004) J. Comput. Chem. , vol.25 , pp. 28-39
- Lu, N.D.¹ Kofke, D.A.² Woolf, T.B.³

35
- 5744249209
- Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J. Chem. Phys. 1953, 21, 1087-1092
- (1953) J. Chem. Phys. , vol.21 , pp. 1087-1092
- Metropolis, N.¹ Rosenbluth, A.W.² Rosenbluth, M.N.³ Teller, A.H.⁴ Teller, E.⁵

36
- 1842607440
- Simonson, T.; Carlsson, J.; Case, D. A. J. Am. Chem. Soc. 2004, 126, 4167-4180
- (2004) J. Am. Chem. Soc. , vol.126 , pp. 4167-4180
- Simonson, T.¹ Carlsson, J.² Case, D.A.³

37
- 0027219184
- Bashford, D.; Case, D. A.; Dalvit, C.; Tennant, L.; Wright, P. E. Biochemistry 1993, 32, 8045-8056
- (1993) Biochemistry , vol.32 , pp. 8045-8056
- Bashford, D.¹ Case, D.A.² Dalvit, C.³ Tennant, L.⁴ Wright, P.E.⁵

38
- 0025319619
- Katti, S. K.; Lemaster, D. M.; Eklund, H. J. Mol. Biol. 1990, 212, 167-184
- (1990) J. Mol. Biol. , vol.212 , pp. 167-184
- Katti, S.K.¹ Lemaster, D.M.² Eklund, H.³

39
- 58049201323
- University of California: San Francisco
- Case, D. A.; Darden, T. A.; Cheatham, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; B.;, W.; Hayik, S.; Roitberg, A. E.; Seabra, G.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. AMBER 10; University of California: San Francisco, 2008.
- (2008) AMBER 10
- Case, D.A.¹ Darden, T.A.² Cheatham, T.E.³ Simmerling, C.L.⁴ Wang, J.⁵ Duke, R.E.⁶ Luo, R.⁷ Crowley, M.⁸ Walker, R.C.⁹ Zhang, W.¹⁰ Merz, K.M.B.W.¹¹ Hayik, S.¹² Roitberg, A.E.¹³ Seabra, G.¹⁴ Kolossváry, I.¹⁵ Wong, K.F.¹⁶ Paesani, F.¹⁷ Vanicek, J.¹⁸ Brozell, S.R.¹⁹ Steinbrecher, T.²⁰ more..

40
- 33748518255
- Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins: Struct., Funct., Bioinf. 2006, 65, 712-725
- (2006) Proteins: Struct., Funct., Bioinf. , vol.65 , pp. 712-725
- Hornak, V.¹ Abel, R.² Okur, A.³ Strockbine, B.⁴ Roitberg, A.⁵ Simmerling, C.⁶

41
- 33646940952
- Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341
- (1977) J. Comput. Phys. , vol.23 , pp. 327-341
- Ryckaert, J.P.¹ Ciccotti, G.² Berendsen, H.J.C.³

42
- 0037110472
- Onufriev, A.; Case, D. A.; Bashford, D. J. Comput. Chem. 2002, 23, 1297-1304
- (2002) J. Comput. Chem. , vol.23 , pp. 1297-1304
- Onufriev, A.¹ Case, D.A.² Bashford, D.³

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.