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Journal of Chemical Theory and Computation

Volumn 6, Issue 6, 2010, Pages 1884-1893

Accurate estimates of free energy changes in charge mutations

(2) Morgan, Brittany R a Massi, Francesca b

a CLARK UNIVERSITY (United States)

b UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77953297597 PISSN: 15499618 EISSN: 15499626 Source Type: Journal
DOI: 10.1021/ct900565e Document Type: Article

Times cited : (16)

References (65)

1
- 0024578173
- Beveridge, D. L.; Dicapua, F. M. Annu. Rev. Biophys. Biophys. Chem. 1989, 18, 431-492
- (1989) Annu. Rev. Biophys. Biophys. Chem. , vol.18 , pp. 431-492
- Beveridge, D.L.¹ Dicapua, F.M.²

2
- 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

3
- 0037736706
- Chipot, C.; Pearlman, D. A. Mol. Simul. 2002, 28, 1-12
- (2002) Mol. Simul. , vol.28 , pp. 1-12
- Chipot, C.¹ Pearlman, D.A.²

4
- 0023346161
- Bash, P. A.; Singh, U. C.; Langridge, R.; Kollman, P. A. Science 1987, 236, 564-568
- (1987) Science , vol.236 , pp. 564-568
- Bash, P.A.¹ Singh, U.C.² Langridge, R.³ Kollman, P.A.⁴

5
- 33751198084
- Dixit, S. B.; Bhasin, R.; Rajasekaran, E.; Jayaram, B. J. Chem. Soc., Faraday Trans. 1997, 93, 1105-1113
- (1997) J. Chem. Soc., Faraday Trans. , vol.93 , pp. 1105-1113
- Dixit, S.B.¹ Bhasin, R.² Rajasekaran, E.³ Jayaram, B.⁴

6
- 24144479792
- Shirts, M. R.; Pande, V. S. J. Chem. Phys. 2005, 122, 134508-134508-13
- (2005) J. Chem. Phys. , vol.122 , pp. 134508-13450813
- Shirts, M.R.¹ Pande, V.S.²

7
- 33746508990
- Bren, U.; Martinek, V.; Florian, J. J. Phys. Chem. B 2006, 110, 12782-12788
- (2006) J. Phys. Chem. B , vol.110 , pp. 12782-12788
- Bren, U.¹ Martinek, V.² Florian, J.³

8
- 7544232432
- Deng, Y. Q.; Roux, B. J. Phys. Chem. B 2004, 108, 16567-16576
- (2004) J. Phys. Chem. B , vol.108 , pp. 16567-16576
- Deng, Y.Q.¹ Roux, B.²

9
- 65249147164
- Shivakumar, D.; Deng, Y. Q.; Roux, B. J. Chem. Theory Comput. 2009, 5, 919-930
- (2009) J. Chem. Theory Comput. , vol.5 , pp. 919-930
- Shivakumar, D.¹ Deng, Y.Q.² Roux, B.³

10
- 58149147138
- Zhou, R. H.; Das, P.; Royyuru, A. K. J. Phys. Chem. B 2008, 112, 15813-15820
- (2008) J. Phys. Chem. B , vol.112 , pp. 15813-15820
- Zhou, R.H.¹ Das, P.² Royyuru, A.K.³

11
- 12344251152
- Donnini, S.; Mark, A. E.; Juffer, A. H.; Villa, A. J. Comput. Chem. 2005, 26, 115-122
- (2005) J. Comput. Chem. , vol.26 , pp. 115-122
- Donnini, S.¹ Mark, A.E.² Juffer, A.H.³ Villa, A.⁴

12
- 67650474076
- Das, P.; Li, J. Y.; Royyuru, A. K.; Zhou, R. H. J. Comput. Chem. 2009, 30, 1654-1663
- (2009) J. Comput. Chem. , vol.30 , pp. 1654-1663
- Das, P.¹ Li, J.Y.² Royyuru, A.K.³ Zhou, R.H.⁴

13
- 0036447407
- Michielin, O.; Karplus, M. J. Mol. Biol. 2002, 324, 547-569
- (2002) J. Mol. Biol. , vol.324 , pp. 547-569
- Michielin, O.¹ Karplus, M.²

14
- 0035950796
- Dixit, S. B.; Chipot, C. J. Phys. Chem. A 2001, 105, 9795-9799
- (2001) J. Phys. Chem. A , vol.105 , pp. 9795-9799
- Dixit, S.B.¹ Chipot, C.²

15
- 35948998959
- Pan, Y. M.; Gao, D. Q.; Yang, W. C.; Cho, H.; Zhan, C. G. J. Am. Chem. Soc. 2007, 129, 13537-13543
- (2007) J. Am. Chem. Soc. , vol.129 , pp. 13537-13543
- Pan, Y.M.¹ Gao, D.Q.² Yang, W.C.³ Cho, H.⁴ Zhan, C.G.⁵

16
- 65249124122
- Deng, Y. Q.; Roux, B. J. Phys. Chem. B 2009, 113, 2234-2246
- (2009) J. Phys. Chem. B , vol.113 , pp. 2234-2246
- Deng, Y.Q.¹ Roux, B.²

17
- 0003399724
- Free energy calculations
- 2nd ed.; Elsevier: San Diego, CA
- Frenkel, D.; Smit, B. Free energy calculations. In Understanding molecular simulation: from algorithms to applications, 2nd ed.; Elsevier: San Diego, CA, 1996; pp 167-171.
- (1996) Understanding Molecular Simulation: From Algorithms to Applications , pp. 167-171
- Frenkel, D.¹ Smit, B.²

18
- 0141827417
- Free energy estimation
- Oxford University Press: New York
- Allen, M. P.; Tildesley, D. J. Free energy estimation. In Computer simulation of liquids; Oxford University Press: New York, 1987; pp 213-219.
- (1987) Computer Simulation of Liquids , pp. 213-219
- Allen, M.P.¹ Tildesley, D.J.²

19
- 0024365336
- Gao, J.; Kuczera, K.; Tidor, B.; Karplus, M. Science 1989, 244, 1069-1072
- (1989) Science , vol.244 , pp. 1069-1072
- Gao, J.¹ Kuczera, K.² Tidor, B.³ Karplus, M.⁴

20
- 7044239742
- Kollman, P. Chem. Rev. 1993, 93, 2395-2417
- (1993) Chem. Rev. , vol.93 , pp. 2395-2417
- Kollman, P.¹

21
- 0038683517
- Hunenberger, P. H.; McCammon, J. A. J. Chem. Phys. 1999, 110, 1856-1872
- (1999) J. Chem. Phys. , vol.110 , pp. 1856-1872
- Hunenberger, P.H.¹ McCammon, J.A.²

22
- 0001029719
- Figueirido, F.; Delbuono, G. S.; Levy, R. M. J. Chem. Phys. 1995, 103, 6133-6142
- (1995) J. Chem. Phys. , vol.103 , pp. 6133-6142
- Figueirido, F.¹ Delbuono, G.S.² Levy, R.M.³

23
- 0001457283
- Sakane, S.; Ashbaugh, H. S.; Wood, R. H. J. Phys. Chem. B 1998, 102, 5673-5682
- (1998) J. Phys. Chem. B , vol.102 , pp. 5673-5682
- Sakane, S.¹ Ashbaugh, H.S.² Wood, R.H.³

24
- 0000123071
- Bogusz, S.; Cheatham, T. E.; Brooks, B. R. J. Chem. Phys. 1998, 108, 7070-7084
- (1998) J. Chem. Phys. , vol.108 , pp. 7070-7084
- Bogusz, S.¹ Cheatham, T.E.² Brooks, B.R.³

25
- 34547854183
- Kastenholz, M. A.; Hunenberger, P. H. J. Chem. Phys. 2006, 124, 124106-124106-27
- (2006) J. Chem. Phys. , vol.124 , pp. 124106-12410627
- Kastenholz, M.A.¹ Hunenberger, P.H.²

26
- 33745155379
- Kastenholz, M. A.; Hunenberger, P. H. J. Chem. Phys. 2006, 124, 224501-224501-20
- (2006) J. Chem. Phys. , vol.124 , pp. 224501-22450120
- Kastenholz, M.A.¹ Hunenberger, P.H.²

27
- 0001570192
- Aqvist, J.; Hansson, T. J. Phys. Chem. B 1998, 102, 3837-3840
- (1998) J. Phys. Chem. B , vol.102 , pp. 3837-3840
- Aqvist, J.¹ Hansson, T.²

28
- 0001382020
- Aqvist, J. J. Comput. Chem. 1996, 17, 1587-1597
- (1996) J. Comput. Chem. , vol.17 , pp. 1587-1597
- Aqvist, J.¹

29
- 67651225150
- Carlsson, J.; Aqvist, J. J. Phys. Chem. B 2009, 113, 10255-10260
- (2009) J. Phys. Chem. B , vol.113 , pp. 10255-10260
- Carlsson, J.¹ Aqvist, J.²

30
- 33751344549
- Carlsson, J.; Aqvist, J. Phys. Chem. Chem. Phys. 2006, 8, 5385-5395
- (2006) Phys. Chem. Chem. Phys. , vol.8 , pp. 5385-5395
- Carlsson, J.¹ Aqvist, J.²

31
- 0001563899
- Straatsma, T. P.; Berendsen, H. J. C. J. Chem. Phys. 1988, 89, 5876-5886
- (1988) J. Chem. Phys. , vol.89 , pp. 5876-5886
- Straatsma, T.P.¹ Berendsen, H.J.C.²

32
- 0344796204
- Aqvist, J. J. Phys. Chem. 1990, 94, 8021-8024
- (1990) J. Phys. Chem. , vol.94 , pp. 8021-8024
- Aqvist, J.¹

33
- 47949129012
- Haranczyk, M.; Gutowski, M.; Warshel, A. Phys. Chem. Chem. Phys. 2008, 10, 4442-4448
- (2008) Phys. Chem. Chem. Phys. , vol.10 , pp. 4442-4448
- Haranczyk, M.¹ Gutowski, M.² Warshel, A.³

34
- 7044260905
- Jorgensen, W.; Ulmschneider, J.; Tirado-Rives, J. J. Phys. Chem. B 2004, 108, 16264-17270
- (2004) J. Phys. Chem. B , vol.108 , pp. 16264-17270
- Jorgensen, W.¹ Ulmschneider, J.² Tirado-Rives, J.³

35
- 36649023306
- Almlof, M.; Carlsson, J.; Aqvist, J. J. Chem. Theory Comput. 2007, 3, 2162-2175
- (2007) J. Chem. Theory Comput. , vol.3 , pp. 2162-2175
- Almlof, M.¹ Carlsson, J.² Aqvist, J.³

36
- 57849157822
- Harder, E.; Roux, B. J. Chem. Phys. 2008, 129, 234706-234706-9
- (2008) J. Chem. Phys. , vol.129 , pp. 234706-2347069
- Harder, E.¹ Roux, B.²

37
- 33644879448
- Lamoureux, G.; Roux, B. J. Phys. Chem. B 2006, 110, 3308-3322
- (2006) J. Phys. Chem. B , vol.110 , pp. 3308-3322
- Lamoureux, G.¹ Roux, B.²

38
- 33846823909
- Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092
- (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
- Darden, T.¹ York, D.² Pedersen, L.³

39
- 33645961739
- Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593
- (1995) J. Chem. Phys. , vol.103 , pp. 8577-8593
- Essmann, U.¹ Perera, L.² Berkowitz, M.L.³ Darden, T.⁴ Lee, H.⁵ Pedersen, L.G.⁶

40
- 0000577932
- Petersen, H. G. J. Chem. Phys. 1995, 103, 3668-3679
- (1995) J. Chem. Phys. , vol.103 , pp. 3668-3679
- Petersen, H.G.¹

41
- 33751143432
- Hummer, G.; Pratt, L. R.; Garcia, A. E. J. Phys. Chem. 1996, 100, 1206-1215
- (1996) J. Phys. Chem. , vol.100 , pp. 1206-1215
- Hummer, G.¹ Pratt, L.R.² Garcia, A.E.³

42
- 0346850017
- Grossfield, A.; Ren, P. Y.; Ponder, J. W. J. Am. Chem. Soc. 2003, 125, 15671-15682
- (2003) J. Am. Chem. Soc. , vol.125 , pp. 15671-15682
- Grossfield, A.¹ Ren, P.Y.² Ponder, J.W.³

43
- 0031185669
- Figueirido, F.; DelBueno, G. S.; Levy, R. M. J. Phys. Chem. B 1997, 101, 5622-5623
- (1997) J. Phys. Chem. B , vol.101 , pp. 5622-5623
- Figueirido, F.¹ Delbueno, G.S.² Levy, R.M.³

44
- 0033726550
- Rozanska, X.; Chipot, C. J. Chem. Phys. 2000, 112, 9691-9694
- (2000) J. Chem. Phys. , vol.112 , pp. 9691-9694
- Rozanska, X.¹ Chipot, C.²

45
- 0001588185
- Marrone, T. J.; Merz, K. M. J. Phys. Chem. 1993, 97, 6524-6529
- (1993) J. Phys. Chem. , vol.97 , pp. 6524-6529
- Marrone, T.J.¹ Merz, K.M.²

46
- 0001304331
- Deleeuw, S. W.; Perram, J. W.; Smith, E. R. Annu. Rev. Phys. Chem. 1986, 37, 245-270
- (1986) Annu. Rev. Phys. Chem. , vol.37 , pp. 245-270
- Deleeuw, S.W.¹ Perram, J.W.² Smith, E.R.³

47
- 0000285845
- Cichocki, B.; Felderhof, B. U.; Hinsen, K. Phys. Rev. A 1989, 39, 5350-5358
- (1989) Phys. Rev. A , vol.39 , pp. 5350-5358
- Cichocki, B.¹ Felderhof, B.U.² Hinsen, K.³

48
- 0001084325
- Nijboer, B. R. A.; Ruijgrok, T. W. J. Stat. Phys. 1988, 53, 361-382
- (1988) J. Stat. Phys. , vol.53 , pp. 361-382
- Nijboer, B.R.A.¹ Ruijgrok, T.W.²

49
- 0031167555
- Nina, M.; Beglov, D.; Roux, B. J. Phys. Chem. B 1997, 101, 5239-5248
- (1997) J. Phys. Chem. B , vol.101 , pp. 5239-5248
- Nina, M.¹ Beglov, D.² Roux, B.³

50
- 0442310716
- Gomer, R.; Tryson, G. J. Chem. Phys. 1977, 66, 4413-4424
- (1977) J. Chem. Phys. , vol.66 , pp. 4413-4424
- Gomer, R.¹ Tryson, G.²

51
- 0000610069
- Klots, C. E. J. Phys. Chem. 1981, 85, 3585-3588
- (1981) J. Phys. Chem. , vol.85 , pp. 3585-3588
- Klots, C.E.¹

52
- 0033984826
- Schmid, R.; Miah, A. M.; Sapunov, V. N. Phys. Chem. Chem. Phys. 2000, 2, 97-102
- (2000) Phys. Chem. Chem. Phys. , vol.2 , pp. 97-102
- Schmid, R.¹ Miah, A.M.² Sapunov, V.N.³

53
- 0000301294
- Tissandier, M. D.; Cowen, K. A.; Feng, W. Y.; Gundlach, E.; Cohen, M. H.; Earhart, A. D.; Coe, J. V.; Tuttle, T. R. J. Phys. Chem. A 1998, 102, 7787-7794
- (1998) J. Phys. Chem. A , vol.102 , pp. 7787-7794
- Tissandier, M.D.¹ Cowen, K.A.² Feng, W.Y.³ Gundlach, E.⁴ Cohen, M.H.⁵ Earhart, A.D.⁶ Coe, J.V.⁷ Tuttle, T.R.⁸

54
- 0001354381
- Noyes, R. M. J. Am. Chem. Soc. 1962, 84, 513-522
- (1962) J. Am. Chem. Soc. , vol.84 , pp. 513-522
- Noyes, R.M.¹

55
- 37049070010
- Marcus, Y. J. Chem. Soc., Faraday Trans. 1991, 87, 2995-2999
- (1991) J. Chem. Soc., Faraday Trans. , vol.87 , pp. 2995-2999
- Marcus, Y.¹

56
- 0001707752
- Randles, J. E. B. J. Trans. Faraday Soc. 1956, 52, 1573-1581
- (1956) J. Trans. Faraday Soc. , vol.52 , pp. 1573-1581
- Randles, J.E.B.¹

57
- 34547889165
- Warren, G. L.; Patel, S. J. Chem. Phys. 2007, 127 064509-064509-19
- (2007) J. Chem. Phys. , vol.127 , pp. 064509-06450919
- Warren, G.L.¹ Patel, S.²

58
- 0041824707
- Hummer, G.; Pratt, L. R.; Garcia, A. E. J. Chem. Phys. 1997, 107, 9275-9277
- (1997) J. Chem. Phys. , vol.107 , pp. 9275-9277
- Hummer, G.¹ Pratt, L.R.² Garcia, A.E.³

59
- 34548680131
- Chipot, C.; Pohorille, A., Eds. Springer: New York
- Free energy calculations; Chipot, C.; Pohorille, A., Eds.; Springer: New York, 2007.
- (2007) Free Energy Calculations

60
- 77950376898
- Zwanikken, J.; van Roij, R. J. Phys.: Condens. Matter 2009, 21, 424102-424102-6
- (2009) J. Phys.: Condens. Matter , vol.21 , pp. 424102-4241026
- Zwanikken, J.¹ Van Roij, R.²

61
- 1842422919
- Rajamani, S.; Ghosh, T.; Garde, S. J. Chem. Phys. 2004, 120, 4457-4466
- (2004) J. Chem. Phys. , vol.120 , pp. 4457-4466
- Rajamani, S.¹ Ghosh, T.² Garde, S.³

62
- 0038001529
- Lu, N.; Kofke, D. A.; Woolf, T. B. J. Phys. Chem. B 2003, 107, 5598-5611
- (2003) J. Phys. Chem. B , vol.107 , pp. 5598-5611
- Lu, N.¹ Kofke, D.A.² Woolf, T.B.³

63
- 27344436659
- Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802
- (2005) J. Comput. Chem. , vol.26 , pp. 1781-1802
- Phillips, J.C.¹ Braun, R.² Wang, W.³ Gumbart, J.⁴ Tajkhorshid, E.⁵ Villa, E.⁶ Chipot, C.⁷ Skeel, R.D.⁸ Kale, L.⁹ Schulten, K.¹⁰

64
- 0041784950
- MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616
- (1998) J. Phys. Chem. B , vol.102 , pp. 3586-3616
- MacKerell, A.D.¹ Bashford, D.² Bellott, M.³ Dunbrack, R.L.⁴ Evanseck, J.D.⁵ Field, M.J.⁶ Fischer, S.⁷ Gao, J.⁸ Guo, H.⁹ Ha, S.¹⁰ Joseph-Mccarthy, D.¹¹ Kuchnir, L.¹² Kuczera, K.¹³ Lau, F.T.K.¹⁴ Mattos, C.¹⁵ Michnick, S.¹⁶ Ngo, T.¹⁷ Nguyen, D.T.¹⁸ Prodhom, B.¹⁹ Reiher, W.E.²⁰ more..

65
- 84961976132
- Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2006, 110, 16066-16081
- (2006) J. Phys. Chem. B , vol.110 , pp. 16066-16081
- Kelly, C.P.¹ Cramer, C.J.² Truhlar, D.G.³

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