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Journal of Chemical Theory and Computation

Volumn 10, Issue 10, 2014, Pages 4515-4534

Ff14ipq: A self-consistent force field for condensed-phase simulations of proteins

(4) Cerutti, David S a Swope, William C a Rice, Julia E a Case, David A a

a RUTGERS UNIVERSITY (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84907992125 PISSN: 15499618 EISSN: 15499626 Source Type: Journal
DOI: 10.1021/ct500643c Document Type: Article

Times cited : (87)

References (49)

1
- 23444454552
- Case, D.; Cheatham, T.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. J.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. Comput. Chem. 2005, 26, 1668-1688
- (2005) J. Comput. Chem. , vol.26 , pp. 1668-1688
- Case, D.¹ Cheatham, T.² Darden, T.³ Gohlke, H.⁴ Luo, R.⁵ Merz, K.J.⁶ Onufriev, A.⁷ Simmerling, C.⁸ Wang, B.⁹ Woods, R.¹⁰

2
- 39049147617
- Kirschner, K.; Yongye, A.; Tschampel, S.; Gonzáles-Outeiriño, J.; Daniels, C.; Foley, B.; Woods, R. J. Comput. Chem. 2008, 29, 622-655
- (2008) J. Comput. Chem. , vol.29 , pp. 622-655
- Kirschner, K.¹ Yongye, A.² Tschampel, S.³ Gonzáles-Outeiriño, J.⁴ Daniels, C.⁵ Foley, B.⁶ Woods, R.⁷

3
- 33645786604
- Buck, M.; Bouguet-Bonnet, S.; Pastor, R.; MacKerrel, A. Biophys. J. 2006, 90, L36-L38
- (2006) Biophys. J. , vol.90 , pp. L36-L38
- Buck, M.¹ Bouguet-Bonnet, S.² Pastor, R.³ MacKerrel, A.⁴

4
- 84859611714
- Beauchamp, K.; Lin, Y.-S.; Das, R.; Pande, V. J. Chem. Theory Comput. 2012, 8, 1409-1414
- (2012) J. Chem. Theory Comput. , vol.8 , pp. 1409-1414
- Beauchamp, K.¹ Lin, Y.-S.² Das, R.³ Pande, V.⁴

5
- 84865723813
- Best, R.; Xiao Zhu, X.; Shim, J.; Lopes, P.; Mittal, J.; Feig, M.; MacKerell, A. D., Jr. J. Chem. Theory Comput. 2012, 8, 3257-3273
- (2012) J. Chem. Theory Comput. , vol.8 , pp. 3257-3273
- Best, R.¹ Xiao Zhu, X.² Shim, J.³ Lopes, P.⁴ Mittal, J.⁵ Feig, M.⁶ Mackerell, A.D.⁷

6
- 77953377650
- Klauda, J.; Venable, R.; Freites, J.; O'Connor, J.; Tobias, D.; Mondragon-Ramirez, C.; Vorobyov, I.; MacKerell, A.; Pastor, R. J. Phys. Chem. B 2010, 114, 7830
- (2010) J. Phys. Chem. B , vol.114 , pp. 7830
- Klauda, J.¹ Venable, R.² Freites, J.³ O'Connor, J.⁴ Tobias, D.⁵ Mondragon-Ramirez, C.⁶ Vorobyov, I.⁷ MacKerell, A.⁸ Pastor, R.⁹

7
- 33748518255
- Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins 2006, 65, 712-725
- (2006) Proteins , vol.65 , pp. 712-725
- Hornak, V.¹ Abel, R.² Okur, A.³ Strockbine, B.⁴ Roitberg, A.⁵ Simmerling, C.⁶

8
- 33645716062
- Wang, Z.; Zhang, W.; Wu, C.; Lei, H.; P, C.; Duan, Y. J. Comput. Chem. 2005, 27, 781-790
- (2005) J. Comput. Chem. , vol.27 , pp. 781-790
- Wang, Z.¹ Zhang, W.² Wu, C.³ Lei, H.⁴ Duan, Y.⁵

9
- 4444351490
- MacKerell, A., Jr. J. Comput. Chem. 2004, 25, 1584-1604
- (2004) J. Comput. Chem. , vol.25 , pp. 1584-1604
- Mackerell, A.¹

10
- 0029011701
- Cornell, W.; Cieplak, P.; Bayly, C.; Gould, I.; Merz, K. J.; Ferguson, D.; Spellmeyer, D.; Fox, T.; Caldwell, J.; Kollman, P. J. Am. Chem. Soc. 1995, 117, 5179-5197
- (1995) J. Am. Chem. Soc. , vol.117 , pp. 5179-5197
- Cornell, W.¹ Cieplak, P.² Bayly, C.³ Gould, I.⁴ Merz, K.J.⁵ Ferguson, D.⁶ Spellmeyer, D.⁷ Fox, T.⁸ Caldwell, J.⁹ Kollman, P.¹⁰

11
- 3042524904
- Bayly, C.; Cieplak, P.; Cornell, W.; Kollman, P. J. Phys. Chem. 1993, 97, 10269-10280
- (1993) J. Phys. Chem. , vol.97 , pp. 10269-10280
- Bayly, C.¹ Cieplak, P.² Cornell, W.³ Kollman, P.⁴

12
- 0001398008
- Wang, J.; Cieplak, P.; Kollman, P. J. Comput. Chem. 2000, 21, 1049-1074
- (2000) J. Comput. Chem. , vol.21 , pp. 1049-1074
- Wang, J.¹ Cieplak, P.² Kollman, P.³

13
- 0035366784
- Dunning, T. J.; Peterson, K.; Wilson, A. J. Chem. Phys. 2001, 114, 9244-9253
- (2001) J. Chem. Phys. , vol.114 , pp. 9244-9253
- Dunning, T.J.¹ Peterson, K.² Wilson, A.³

14
- 0035879976
- Rassolov, V.; Ratner, M.; Pople, J.; Redfern, P.; Curtiss, L. J. Comput. Chem. 2001, 22, 976
- (2001) J. Comput. Chem. , vol.22 , pp. 976
- Rassolov, V.¹ Ratner, M.² Pople, J.³ Redfern, P.⁴ Curtiss, L.⁵

15
- 3843146349
- Woon, D.; Dunning, T. J. J. Chem. Phys. 1993, 98, 1358-1371
- (1993) J. Chem. Phys. , vol.98 , pp. 1358-1371
- Woon, D.¹ Dunning, T.J.²

16
- 4143095330
- Kendall, R.; Dunning, T. J.; Harrison, R. J. Chem. Phys. 1992, 96, 6796-6806
- (1992) J. Chem. Phys. , vol.96 , pp. 6796-6806
- Kendall, R.¹ Dunning, T.J.² Harrison, R.³

17
- 33746614482
- Dunning, T. J. J. Chem. Phys. 1989, 90, 1007-1023
- (1989) J. Chem. Phys. , vol.90 , pp. 1007-1023
- Dunning, T.J.¹

18
- 0242663237
- Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T. J. Comput. Chem. 2003, 24, 1999-2012
- (2003) J. Comput. Chem. , vol.24 , pp. 1999-2012
- Duan, Y.¹ Wu, C.² Chowdhury, S.³ Lee, M.⁴ Xiong, G.⁵ Zhang, W.⁶ Yang, R.⁷ Cieplak, P.⁸ Luo, R.⁹ Lee, T.¹⁰

19
- 84866164320
- Zgarbová, M.; Luque, F.; ͈poner, J.; Otyepka, M.; Jureɥka, P. J. Chem. Theory Comput. 2012, 8, 3232-3242
- (2012) J. Chem. Theory Comput. , vol.8 , pp. 3232-3242
- Zgarbová, M.¹ Luque, F.² ͈poner, J.³ Otyepka, M.⁴ Jureɥka, P.⁵

20
- 84874604927
- Cerutti, D.; Swope, W.; Rice, J.; Case, D. J. Phys. Chem. B 2013, 117, 2328-2338
- (2013) J. Phys. Chem. B , vol.117 , pp. 2328-2338
- Cerutti, D.¹ Swope, W.² Rice, J.³ Case, D.⁴

21
- 84891727890
- Karamertzanis, P.; Raiteri, P.; Galindo, A. J. Chem. Theory Comput. 2010, 6, 3153-3161
- (2010) J. Chem. Theory Comput. , vol.6 , pp. 3153-3161
- Karamertzanis, P.¹ Raiteri, P.² Galindo, A.³

22
- 2942622288
- Horn, H.; Swope, W.; Pitera, J.; Madura, J.; Dick, T.; Hura, G.; Head-Gordon, T. J. Chem. Phys. 2004, 120, 9665-9678
- (2004) J. Chem. Phys. , vol.120 , pp. 9665-9678
- Horn, H.¹ Swope, W.² Pitera, J.³ Madura, J.⁴ Dick, T.⁵ Hura, G.⁶ Head-Gordon, T.⁷

23
- 0033716531
- Badyal, Y.; Saboungi, M.; Price, D.; Shastri, S.; Haeffner, D.; Soper, A. J. Chem. Phys. 2000, 112, 9206-9208
- (2000) J. Chem. Phys. , vol.112 , pp. 9206-9208
- Badyal, Y.¹ Saboungi, M.² Price, D.³ Shastri, S.⁴ Haeffner, D.⁵ Soper, A.⁶

24
- 84986514852
- Nobes, R.; Rodwell, W.; Radom, L. J. Comput. Chem. 2004, 3, 561-564
- (2004) J. Comput. Chem. , vol.3 , pp. 561-564
- Nobes, R.¹ Rodwell, W.² Radom, L.³

25
- 84873695685
- Reif, M.; Winger, M.; Oostenbrink, C. J. Chem. Theory Comput. 2013, 9, 1247-1264
- (2013) J. Chem. Theory Comput. , vol.9 , pp. 1247-1264
- Reif, M.¹ Winger, M.² Oostenbrink, C.³

26
- 79959999377
- E; Simon, S.; Marquant, G.; Garcia, E.; Klimerak, G.; Delepine, J.; Cieplak, P.; Dupradeau, F.-Y. Nucleic Acids Res. 2011, 39, W511-W517
- (2011) Nucleic Acids Res. , vol.39 , pp. W511-W517
- Simon, S.¹ Marquant, G.² Garcia, E.³ Klimerak, G.⁴ Delepine, J.⁵ Cieplak, P.⁶ Dupradeau, F.-Y.⁷

27
- 77954566051
- Dupradeau, F.-Y.; Pigache, A.; Zaffran, T.; Savineau, C.; Lelong, R.; Grivel, N.; Lelong, D.; Rosanski, W.; Cieplak, P. Phys. Chem. Chem. Phys. 2010, 12, 7821-7839
- (2010) Phys. Chem. Chem. Phys. , vol.12 , pp. 7821-7839
- Dupradeau, F.-Y.¹ Pigache, A.² Zaffran, T.³ Savineau, C.⁴ Lelong, R.⁵ Grivel, N.⁶ Lelong, D.⁷ Rosanski, W.⁸ Cieplak, P.⁹

28
- 70450206724
- Revision D.01; Gaussian Inc. Wallingford, CT.
- Frisch, M. Gaussian 09, Revision D.01; Gaussian Inc.: Wallingford, CT, 2009.
- (2009) Gaussian 09
- Frisch, M.¹

29
- 84859061927
- Neese, F. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2012, 2, 73-78
- (2012) Wiley Interdiscip. Rev.: Comput. Mol. Sci. , vol.2 , pp. 73-78
- Neese, F.¹

30
- 1842479952
- Onufriev, A.; Bashford, D.; Case, D. Proteins 2004, 55, 383-394
- (2004) Proteins , vol.55 , pp. 383-394
- Onufriev, A.¹ Bashford, D.² Case, D.³

31
- 77953513118
- Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J.; Dror, R.; Shaw, D. Proteins 2010, 78, 1950-1958
- (2010) Proteins , vol.78 , pp. 1950-1958
- Lindorff-Larsen, K.¹ Piana, S.² Palmo, K.³ Maragakis, P.⁴ Klepeis, J.⁵ Dror, R.⁶ Shaw, D.⁷

32
- 4143145167
- Honda, S.; Yamasaki, K.; Sawada, Y.; Morii, H. Structure 2004, 12, 1507-1518
- (2004) Structure , vol.12 , pp. 1507-1518
- Honda, S.¹ Yamasaki, K.² Sawada, Y.³ Morii, H.⁴

33
- 0042367594
- Ulmer, T.; Ramirez, B.; Delaglio, F.; Bax, A. J. Am. Chem. Soc. 2003, 125, 9179-9191
- (2003) J. Am. Chem. Soc. , vol.125 , pp. 9179-9191
- Ulmer, T.¹ Ramirez, B.² Delaglio, F.³ Bax, A.⁴

34
- 0032128284
- Walsh, M.; Schneidr, T.; Sieker, L.; Dauter, Z.; Lamzin, V.; Wilson, K. Acta Crtystallogr., Sect. D 1998, 54, 522-546
- (1998) Acta Crtystallogr., Sect. D , vol.54 , pp. 522-546
- Walsh, M.¹ Schneidr, T.² Sieker, L.³ Dauter, Z.⁴ Lamzin, V.⁵ Wilson, K.⁶

35
- 33646940952
- Ryckaert, J.; Ciccotti, G.; Berendsen, H.; Hirasawa, K. J. Comput. Phys. 1977, 23, 327-341
- (1977) J. Comput. Phys. , vol.23 , pp. 327-341
- Ryckaert, J.¹ Ciccotti, G.² Berendsen, H.³ Hirasawa, K.⁴

36
- 84986440341
- Miyamoto, S.; Kollman, P. J. Comput. Chem. 1992, 13, 952-962
- (1992) J. Comput. Chem. , vol.13 , pp. 952-962
- Miyamoto, S.¹ Kollman, P.²

37
- 0034817509
- Izaguirre, J.; Catarello, D.; Wozniak, J.; Skeel, R. J. Chem. Phys. 2001, 114, 2090-2098
- (2001) J. Chem. Phys. , vol.114 , pp. 2090-2098
- Izaguirre, J.¹ Catarello, D.² Wozniak, J.³ Skeel, R.⁴

38
- 46749127364
- Best, R.; Buchete, N.-V.; Hummer, G. Biophys. J. 2008, 108, L07
- (2008) Biophys. J. , vol.108 , pp. 07
- Best, R.¹ Buchete, N.-V.² Hummer, G.³

39
- 33846783019
- Graf, J.; Nguyen, P.; Stock, G.; Schwalbe, H. J. Am. Chem. Soc. 2007, 129, 1179-1189
- (2007) J. Am. Chem. Soc. , vol.129 , pp. 1179-1189
- Graf, J.¹ Nguyen, P.² Stock, G.³ Schwalbe, H.⁴

40
- 0034715485
- Case, D.; Scheurer, C.; BruÌschweiler, R. J. Am. Chem. Soc. 2000, 122, 10390-10397
- (2000) J. Am. Chem. Soc. , vol.122 , pp. 10390-10397
- Case, D.¹ Scheurer, C.² Bruìschweiler, R.³

41
- 0034645735
- Honda, S.; Kobayashi, N.; Munekata, E. J. Mol. Biol. 2000, 295, 269-278
- (2000) J. Mol. Biol. , vol.295 , pp. 269-278
- Honda, S.¹ Kobayashi, N.² Munekata, E.³

42
- 0034733005
- Kobayashi, N.; Honda, S.; Yoshii, H.; Munekata, E. Biochemistry 2000, 39, 6564-6571
- (2000) Biochemistry , vol.39 , pp. 6564-6571
- Kobayashi, N.¹ Honda, S.² Yoshii, H.³ Munekata, E.⁴

43
- 0038502170
- Muñoz, V.; Thompson, P.; Hofrichter, J.; Eaton, W. Nature 1997, 390, 196-199
- (1997) Nature , vol.390 , pp. 196-199
- Muñoz, V.¹ Thompson, P.² Hofrichter, J.³ Eaton, W.⁴

44
- 49649105768
- Song, K.; Stewart, J.; Fesinmeyer, R.; Andersen, N.; Simmerling, C. Biopolymers 2008, 89, 747-760
- (2008) Biopolymers , vol.89 , pp. 747-760
- Song, K.¹ Stewart, J.² Fesinmeyer, R.³ Andersen, N.⁴ Simmerling, C.⁵

45
- 0036264492
- Neidigh, J.; Fesinmeyer, R.; Andersen, N. Nat. Struct. Biol. 2002, 9, 425-430
- (2002) Nat. Struct. Biol. , vol.9 , pp. 425-430
- Neidigh, J.¹ Fesinmeyer, R.² Andersen, N.³

46
- 2942625637
- Liu, Y.; Liu, Z.; Androphy, E.; Chen, J.; Baleja, J. Biochemistry 2004, 43, 7421-7431
- (2004) Biochemistry , vol.43 , pp. 7421-7431
- Liu, Y.¹ Liu, Z.² Androphy, E.³ Chen, J.⁴ Baleja, J.⁵

47
- 84875225459
- Zeng, J.; Duan, L.; Zhang, J. J. Comput. Chem. 2013, 34, 847-853
- (2013) J. Comput. Chem. , vol.34 , pp. 847-853
- Zeng, J.¹ Duan, L.² Zhang, J.³

48
- 84898427440
- Goetz, A.; Bucher, D.; Lindert, S.; McCammon, J. J. Chem. Theory Comput. 2014, 10, 1631-1637
- (2014) J. Chem. Theory Comput. , vol.10 , pp. 1631-1637
- Goetz, A.¹ Bucher, D.² Lindert, S.³ McCammon, J.⁴

49
- 84902978469
- Debiec, K.; Gronenborn, A.; Chong, L. J. Phys. Chem. B 2014, 118, 6561-6569
- (2014) J. Phys. Chem. B , vol.118 , pp. 6561-6569
- Debiec, K.¹ Gronenborn, A.² Chong, L.³

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