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Journal of Computational Chemistry

Volumn 34, Issue 31, 2013, Pages 2726-2741

Absolute free energies of biomolecules from unperturbed ensembles

(1) Grigoryan, Gevorg a

a Dartmouth Department of Computer Science_Dartmouth College (United States)

Author keywords

absolute free energy; computational protein design; conformational state; random energy model

Indexed keywords

COMPUTATIONAL PROTEIN DESIGN; CONFORMATIONAL STATE; FREE-ENERGY DIFFERENCE; LOCAL CONFIGURATIONS; MOLECULAR DYNAMICS SIMULATIONS; RANDOM ENERGY MODELS; SOLVATION FREE ENERGIES; TEMPLATE STRUCTURES;

AMINO ACIDS; BIOCHEMICAL ENGINEERING; COMPUTER SIMULATION; FREE ENERGY; MACROMOLECULES;

STRUCTURAL DESIGN;

AMINO ACID; PEPTIDE;

ABSOLUTE FREE ENERGY; ARTICLE; CHEMISTRY; COMPUTATIONAL PROTEIN DESIGN; CONFORMATIONAL STATE; MOLECULAR DYNAMICS; PROTEIN SECONDARY STRUCTURE; RANDOM ENERGY MODEL; THERMODYNAMICS;

ABSOLUTE FREE ENERGY; COMPUTATIONAL PROTEIN DESIGN; CONFORMATIONAL STATE; RANDOM ENERGY MODEL;

AMINO ACIDS; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS;

EID: 84886598776 PISSN: 01928651 EISSN: 1096987X Source Type: Journal
DOI: 10.1002/jcc.23448 Document Type: Article

Times cited : (11)

References (66)

1
- 34547127612
- M. A. Stiffler, J. R. Chen, V. P. Grantcharova, Y. Lei, D. Fuchs, J. E. Allen, L. A. Zaslavskaia, G. MacBeath, Science 2007, 317, 364.
- (2007) Science , vol.317 , pp. 364
- Stiffler, M.A.¹ Chen, J.R.² Grantcharova, V.P.³ Lei, Y.⁴ Fuchs, D.⁵ Allen, J.E.⁶ Zaslavskaia, L.A.⁷ MacBeath, G.⁸

2
- 47649130715
- K. M. Armstrong, F. K. Insaidoo, B. M. Baker, J. Mol. Recognit. 2008, 21, 275.
- (2008) J. Mol. Recognit. , vol.21 , pp. 275
- Armstrong, K.M.¹ Insaidoo, F.K.² Baker, B.M.³

3
- 77952312935
- S. Dutta, S. Gullá, T. S. Chen, E. Fire, R. A. Grant, A. E. Keating, J. Mol. Biol. 2010, 398, 747.
- (2010) J. Mol. Biol. , vol.398 , pp. 747
- Dutta, S.¹ Gullá, S.² Chen, T.S.³ Fire, E.⁴ Grant, R.A.⁵ Keating, A.E.⁶

4
- 7444240741
- S. Brauchi, P. Orio, R. Latorre, Proc. Natl. Acad. Sci. USA 2004, 101, 15494.
- (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 15494
- Brauchi, S.¹ Orio, P.² Latorre, R.³

5
- 79959720287
- S. Piana, K. Lindorff-Larsen, D. E. Shaw, Biophys. J. 2011, 100, L47.
- (2011) Biophys. J. , vol.100
- Piana, S.¹ Lindorff-Larsen, K.² Shaw, D.E.³

6
- 77952390528
- C. D. Christ, A. E. Mark, W. F. van Gunsteren, J. Comput. Chem. 2010, 31, 1569.
- (2010) J. Comput. Chem. , vol.31 , pp. 1569
- Christ C, D.¹ Mark, A.E.² Van Gunsteren, W.F.³

7
- 76649086691
- A. Aleksandrova, D. Thompsonb, T. Simonson, J. Mol. Recognit. 2010, 23, 117.
- (2010) J. Mol. Recognit. , vol.23 , pp. 117
- Aleksandrova, A.¹ Thompsonb, D.² Simonson, T.³

8
- 18744372751
- H. -J. Woo, B. Roux, Proc. Natl. Acad. Sci. USA 2004, 102, 6825.
- (2004) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 6825
- Woo, H.-J.¹ Roux, B.²

9
- 44049091290
- D. Jiao, P. A. Golubkov, T. A. Darden, P. Ren, Proc. Natl. Acad. Sci. USA 2008, 105, 6290.
- (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 6290
- Jiao, D.¹ Golubkov, P.A.² Darden, T.A.³ Ren, P.⁴

10
- 77956206604
- P. I. Zhuravlev, S. Wu, D. A. Potoyan, M. Rubinstein, G. A. Papoian, Methods 2010, 52, 115.
- (2010) Methods , vol.52 , pp. 115
- Zhuravlev, P.I.¹ Wu, S.² Potoyan, D.A.³ Rubinstein, M.⁴ Papoian, G.A.⁵

11
- 33846946504
- D. Branduardi, F. L. Gervasio, M. Parrinello, J. Chem. Phys. 2007, 126, 054103.
- (2007) J. Chem. Phys. , vol.126 , pp. 054103
- Branduardi, D.¹ Gervasio, F.L.² Parrinello, M.³

12
- 34147133371
- M. Meirovitch, Curr. Opin. Struct. Biol. 2007, 17, 181.
- (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 181
- Meirovitch, M.¹

13
- 0000127140
- M. Karplus, J. N. Kushick, Macromolecules 1981, 14, 325.
- (1981) Macromolecules , vol.14 , pp. 325
- Karplus, M.¹ Kushick, J.N.²

14
- 25844492293
- C. E. Chang, W. Chen, M. K. Gilson, J. Chem. Theory Comput. 2005, 1, 1017.
- (2005) J. Chem. Theory Comput. , vol.1 , pp. 1017
- Chang, C.E.¹ Chen, W.² Gilson, M.K.³

15
- 33846307768
- J. Wang, R. Brüschweiler, J. Chem. Theory Comput. 2006, 2, 18.
- (2006) J. Chem. Theory Comput. , vol.2 , pp. 18
- Wang, J.¹ Brüschweiler, R.²

16
- 34547648559
- F. M. Ytreberga, D. M. Zuckermanb, J. Chem. Phys. 2006, 124, 104105.
- (2006) J. Chem. Phys. , vol.124 , pp. 104105
- Ytreberga, F.M.¹ Zuckermanb, D.M.²

17
- 33748807193
- M. D. Tyka, A. R. Clarke, R. B. Sessions, J. Chem. Phys. B 2006, 110, 17212.
- (2006) J. Chem. Phys. B , vol.110 , pp. 17212
- Tyka, M.D.¹ Clarke, A.R.² Sessions, R.B.³

18
- 0031079364
- M. S. Head, J. A. Given, M. K. Gilson, J. Phys. Chem. A 2006, 101, 1609.
- (2006) J. Phys. Chem. A , vol.101 , pp. 1609
- Head, M.S.¹ Given, J.A.² Gilson, M.K.³

19
- 84886585026
- S. Cheluvaraja, H. Meirovitch, J. Chem. Phys. 2006, 125, 104105.
- (2006) J. Chem. Phys. , vol.125 , pp. 104105
- Cheluvaraja, S.¹ Meirovitch, H.²

20
- 11144269103
- P. R. White, H. Meirovitch, J. Chem. Phys. 2004, 21, 10889.
- (2004) J. Chem. Phys. , vol.21 , pp. 10889
- White, P.R.¹ Meirovitch, H.²

21
- 79952354508
- Y. A. Lau, B. Roux, Nat. Struct. Mol. Biol. 2010, 18, 283.
- (2010) Nat. Struct. Mol. Biol. , vol.18 , pp. 283
- Lau, Y.A.¹ Roux, B.²

22
- 78650546908
- H. Yu, S. Y. Noskov, B. Roux, Proc. Natl. Acad. Sci. USA 2010, 107, 20329.
- (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 20329
- Yu, H.¹ Noskov, S.Y.² Roux, B.³

23
- 33745620457
- G. Grigoryan, F. Zhou, S. R. Lustig, G. Ceder, D. Morgan, A. E. Keating, PLoS Comput. Biol. 2006, 2, e63.
- (2006) PLoS Comput. Biol. , vol.2
- Grigoryan, G.¹ Zhou, F.² Lustig, S.R.³ Ceder, G.⁴ Morgan, D.⁵ Keating, A.E.⁶

24
- 84886588809
- Wiley: New York, p.
- D. B. Ripley, In Stochastic Simulation, chapter 5; Wiley: New York, 1987; p. 122.
- (1987) Stochastic Simulation, Chapter 5 , pp. 122
- Ripley, D.B.¹

25
- 0037473066
- C. -E. Chang, M. J. Potter, M. K. Gilson, J. Phys. Chem. B 2003, 107, 1048.
- (2003) J. Phys. Chem. B , vol.107 , pp. 1048
- Chang, C.-E.¹ Potter, M.J.² Gilson, M.K.³

26
- 0342929614
- M. G. Torrie, J. P. Valleau, J. Comput. Phys. 1977, 23, 187.
- (1977) J. Comput. Phys. , vol.23 , pp. 187
- Torrie, M.G.¹ Valleau, J.P.²

27
- 67650500988
- B. R. Brooks, C. L. Brooks 3rd, A.D. Mackerell Jr, L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus, et al. J. Comput. Chem. 2009, 30, 1545.
- (2009) J. Comput. Chem. , vol.30 , pp. 1545
- Brooks, B.R.¹ Brooks III, C.L.² MacKerell, Jr.A.D.³ Nilsson, L.⁴ Petrella, R.J.⁵ Roux, B.⁶ Won, Y.⁷ Archontis, G.⁸ Bartels, C.⁹ Boresch, S.¹⁰ Caflisch, A.¹¹ Caves, L.¹² Cui, Q.¹³ Dinner, A.R.¹⁴ Feig, M.¹⁵ Fischer, S.¹⁶ Gao, J.¹⁷ Hodoscek, M.¹⁸ Im, W.¹⁹ Kuczera, K.²⁰ more..

28
- 27344436659
- J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kalé, K. Schulten, J. Comput. Chem. 2005, 26, 1781.
- (2005) J. Comput. Chem. , vol.26 , pp. 1781
- 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 Kalé, L.⁹ Schulten, K.¹⁰

29
- 0141990949
- R. M. Shirts, J. W. Pietra, W. C. Swope, V. S. Pande, J. Chem. Phys. 2003, 119, 5740.
- (2003) J. Chem. Phys. , vol.119 , pp. 5740
- Shirts, R.M.¹ Pietra, J.W.² Swope, W.C.³ Pande, V.S.⁴

30
- 0018582090
- V. R. Wolfenden, P. M. Cullis, C. C. F. Southgate, Science 1979, 206, 575.
- (1979) Science , vol.206 , pp. 575
- Wolfenden, V.R.¹ Cullis, P.M.² Southgate C C, F.³

31
- 18344362394
- N. Go, H. A. Scheraga, Macromolecules 1976, 9, 535.
- (1976) Macromolecules , vol.9 , pp. 535
- Go, N.¹ Scheraga, H.A.²

32
- 33645903407
- A. Ben-Naim, Y. Marcus, J. Chem. Phys. 1984, 81, 2016.
- (1984) J. Chem. Phys. , vol.81 , pp. 2016
- Ben-Naim, A.¹ Marcus, Y.²

33
- 24144479792
- R. M. Shirts, V. S. Pande, J. Chem. Phys. 2005, 122, 134508.
- (2005) J. Chem. Phys. , vol.122 , pp. 134508
- Shirts, R.M.¹ Pande, V.S.²

34
- 84874098113
- J. Zhang, G. Grigoryan, Methods Enzymol. 2013, 523, 21.
- (2013) Methods Enzymol. , vol.523 , pp. 21
- Zhang, J.¹ Grigoryan, G.²

35
- 79957589641
- G. Grigoryan, Y. H. Kim, R. Acharya, K. Axelrod, R. M. Jain, L. Willis, M. Drndic, J. M. Kikkawa, W. F. DeGrado, Science 2011, 332, 1071.
- (2011) Science , vol.332 , pp. 1071
- Grigoryan, G.¹ Kim, Y.H.² Acharya, R.³ Axelrod, K.⁴ Jain, R.M.⁵ Willis, L.⁶ Drndic, M.⁷ Kikkawa, J.M.⁸ Degrado, W.F.⁹

36
- 0034663722
- C. S. Lovell, J. M. Word, J. S. Richardson, D. C. Richardson, Proteins 2000, 40, 389.
- (2000) Proteins , vol.40 , pp. 389
- Lovell, C.S.¹ Word, J.M.² Richardson, J.S.³ Richardson, D.C.⁴

37
- 34548764385
- G. Grigoryan, A. Ochoa, A. E. Keating, Proteins 2007, 68, 863.
- (2007) Proteins , vol.68 , pp. 863
- Grigoryan, G.¹ Ochoa, A.² Keating, A.E.³

38
- 79953761452
- I. Samish, C. M. MacDermaid, J. M. Perez-Aguilar, J. G. Saven, Annu. Rev. Phys. Chem. 2011, 62, 129.
- (2011) Annu. Rev. Phys. Chem. , vol.62 , pp. 129
- Samish, I.¹ MacDermaid, C.M.² Perez-Aguilar, J.M.³ Saven, J.G.⁴

39
- 0033135638
- T. Lazaridis, M. Karplus, Proteins 1999, 35, 133.
- (1999) Proteins , vol.35 , pp. 133
- Lazaridis, T.¹ Karplus, M.²

40
- 0028566270
- G. E. Hutchinson, J. M. Thornton, Protein Sci. 1994, 3, 2207.
- (1994) Protein Sci. , vol.3 , pp. 2207
- Hutchinson, G.E.¹ Thornton, J.M.²

41
- 0025222978
- T. K. O'Neil, W. F. DeGrado, Science 1990, 250, 646.
- (1990) Science , vol.250 , pp. 646
- O'Neil, T.K.¹ Degrado, W.F.²

42
- 0023449962
- D. J. Bryngelson, P. G. Wolynes, Proc. Natl. Acad. Sci. USA 1987, 84, 7524.
- (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 7524
- Bryngelson, D.J.¹ Wolynes, P.G.²

43
- 35949021286
- B. Derrida, Phys. Rev. Lett. 1980, 45, 79.
- (1980) Phys. Rev. Lett. , vol.45 , pp. 79
- Derrida, B.¹

44
- 0028947257
- D. J. Bryngelson, J. N. Onuchic, N. D. Socci, P. G. Wolynes, Proteins 1995, 21, 167.
- (1995) Proteins , vol.21 , pp. 167
- Bryngelson, D.J.¹ Onuchic, J.N.² Socci, N.D.³ Wolynes, P.G.⁴

45
- 0027438090
- I. E. Shakhnovich, A. M. Gutin, Protein Eng. 1993, 6, 793.
- (1993) Protein Eng. , vol.6 , pp. 793
- Shakhnovich, I.E.¹ Gutin, A.M.²

46
- 0000997402
- D. J. Bryngelson, J. Chem. Phys. 1994, 100, 6038.
- (1994) J. Chem. Phys. , vol.100 , pp. 6038
- Bryngelson, D.J.¹

47
- 0001222466
- S. V. Pande, A. Y. Grosberg, T. Tanaka, J. Chem. Phys. 1995, 103, 9482.
- (1995) J. Chem. Phys. , vol.103 , pp. 9482
- Pande, S.V.¹ Grosberg, A.Y.² Tanaka, T.³

48
- 0004260243
- W. H. Freeman and Company: New York
- M. Karplus, E. Shakhnovich, In Protein Folding; W. H. Freeman and Company: New York, 1992; pp. 127-195.
- (1992) Protein Folding , pp. 127-195
- Karplus, M.¹ Shakhnovich, E.²

49
- 36549097257
- I. E. Shakhnovich, A. M. Gutin, J. Chem. Phys., 1990, 93, 5967.
- (1990) J. Chem. Phys. , vol.93 , pp. 5967
- Shakhnovich, I.E.¹ Gutin, A.M.²

50
- 0024357911
- I. E. Shakhnovich, A. M. Gutin, Biophys. Chem. 1989, 34, 187.
- (1989) Biophys. Chem. , vol.34 , pp. 187
- Shakhnovich, I.E.¹ Gutin, A.M.²

51
- 0141816814
- S. Robic, M. Guzman-Casado, J. M. Sanchez-Ruiz, S. Marqusee, Proc. Natl. Acad. Sci. USA 2003, 100, 11345.
- (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 11345
- Robic, S.¹ Guzman-Casado, M.² Sanchez-Ruiz, J.M.³ Marqusee, S.⁴

52
- 1642312065
- K. Lindorff-Larsen, S. Kristjansdottir, K. Teilum, W. Fieber, C. M. Dobson, F. M. Poulsen, M. Vendruscolo, J. Am. Chem. Soc. 2003, 126, 3291.
- (2003) J. Am. Chem. Soc. , vol.126 , pp. 3291
- Lindorff-Larsen, K.¹ Kristjansdottir, S.² Teilum, K.³ Fieber, W.⁴ Dobson, C.M.⁵ Poulsen, F.M.⁶ Vendruscolo, M.⁷

53
- 28844499162
- F. Zhou, G. Grigoryan, S. R. Lustig, A. E. Keating, G. Ceder, D. Morgan, Phys. Rev. Lett. 2005, 95, 148103.
- (2005) Phys. Rev. Lett. , vol.95 , pp. 148103
- Zhou, F.¹ Grigoryan, G.² Lustig, S.R.³ Keating, A.E.⁴ Ceder, G.⁵ Morgan, D.⁶

54
- 79952117766
- S. Hahn, O. Ashenberg, G. Grigoryan, A. E. Keating, J. Comput. Chem. 2010, 31, 2900.
- (2010) J. Comput. Chem. , vol.31 , pp. 2900
- Hahn, S.¹ Ashenberg, O.² Grigoryan, G.³ Keating, A.E.⁴

55
- 0035826776
- G. A. Cochran, N. J. Skelton, M. A. Starovasnik, Proc. Natl. Acad. Sci. USA 2001, 98, 5578.
- (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 5578
- Cochran, G.A.¹ Skelton, N.J.² Starovasnik, M.A.³

56
- 0034641749
- B. Kuhlman, D. Baker, Proc. Natl. Acad. Sci. USA 2000, 97, 10383.
- (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 10383
- Kuhlman, B.¹ Baker, D.²

57
- 84886590171
- H. H. Richard, J. Chem. Phys. 2003, 119, 400.
- (2003) J. Chem. Phys. , vol.119 , pp. 400
- Richard, H.H.¹

58
- 0028834210
- V. Munoz, L. Serrano, J. Mol. Biol. 1995, 245, 297.
- (1995) J. Mol. Biol. , vol.245 , pp. 297
- Munoz, V.¹ Serrano, L.²

59
- 0025222978
- T. K. O'Neil, W. F. DeGrado, Science 1990, 250, 646.
- (1990) Science , vol.250 , pp. 646
- O'Neil, T.K.¹ Degrado, W.F.²

60
- 0027236794
- M. Blaber, X. J. Zhang, B. W. Matthews, Science 1993, 260, 1637.
- (1993) Science , vol.260 , pp. 1637
- Blaber, M.¹ Zhang, X.J.² Matthews, B.W.³

61
- 34147169516
- E. F. Boas, P. B. Harbury, Curr. Opin. Struct. Biol. 2007, 17, 199.
- (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 199
- Boas, E.F.¹ Harbury, P.B.²

62
- 33745033790
- L. G. Butterfoss, B. Kuhlman, Annu. Rev. Biophys. Biomol. Struct. 2006, 35, 49.
- (2006) Annu. Rev. Biophys. Biomol. Struct. , vol.35 , pp. 49
- Butterfoss, L.G.¹ Kuhlman, B.²

63
- 84886584761
- B. Kuhlman, G. Dantas, G. C. Ireton, G. Varani, B. L. Stoddard, D. Baker, Methods Enzymol. 2011, 487, 545.
- (2011) Methods Enzymol. , vol.487 , pp. 545
- Kuhlman, B.¹ Dantas, G.² Ireton, G.C.³ Varani, G.⁴ Stoddard, B.L.⁵ Baker, D.⁶

64
- 79956017135
- J. S. Fleishman, T. A. Whitehead, D. C. Ekiert, C. Dreyfus, J. E. Corn, E. M. Strauch, I. A. Wilson, D. Baker, Science 2011, 332, 816.
- (2011) Science , vol.332 , pp. 816
- Fleishman, J.S.¹ Whitehead, T.A.² Ekiert, D.C.³ Dreyfus, C.⁴ Corn, J.E.⁵ Strauch, E.M.⁶ Wilson, I.A.⁷ Baker, D.⁸

65
- 77954811495
- B. J. Siegel, A. Zanghellini, H. M. Lovick, G. Kiss, A. R. Lambert, J. L. St Clair, J. L. Gallaher, D. Hilvert, M. H. Gelb, B. L. Stoddard, K. N. Houk, F. E. Michael, D. Baker, Science, 2010, 329, 309.
- (2010) Science , vol.329 , pp. 309
- Siegel, B.J.¹ Zanghellini, A.² Lovick, H.M.³ Kiss, G.⁴ Lambert, A.R.⁵ St Clair, J.L.⁶ Gallaher, J.L.⁷ Hilvert, D.⁸ Gelb, M.H.⁹ Stoddard, B.L.¹⁰ Houk, K.N.¹¹ Michael, F.E.¹² Baker, D.¹³

66
- 78650271909
- L. Vouilleme, P. R. Cushing, R. Volkmer, D. R. Madden, P. Boisguerin, Angew. Chem. Int. Ed. 2010, 49, 9912.
- (2010) Angew. Chem. Int. Ed. , vol.49 , pp. 9912
- Vouilleme, L.¹ Cushing, P.R.² Volkmer, R.³ Madden, D.R.⁴ Boisguerin, P.⁵

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