SCOPUS 정보 검색 플랫폼

Journal of Chemical Theory and Computation

Volumn 7, Issue 7, 2011, Pages 2284-2295

Improved treatment of ligands and coupling effects in empirical calculation and rationalization of p K a values

(4) Søndergaard, Chresten R a Olsson, Mats H M a Rostkowski, Michał a Jensen, Jan H a

a UNIVERSITY OF COPENHAGEN (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79960258119 PISSN: 15499618 EISSN: 15499626 Source Type: Journal
DOI: 10.1021/ct200133y Document Type: Article

Times cited : (1386)

References (54)

1
- 34548288600
- Reddy, A. S.; Pati, S. P.; Kumar, P. P.; Pradeep, H.; Sastry, G. N. Curr. Protein Pept. Sci. 2007, 8, 329-351
- (2007) Curr. Protein Pept. Sci. , vol.8 , pp. 329-351
- Reddy, A.S.¹ Pati, S.P.² Kumar, P.P.³ Pradeep, H.⁴ Sastry, G.N.⁵

2
- 8844263008
- Kitchen, D. B.; Decornez, H.; Furr, J. R.; Bajorath, J. Nat. Rev. Drug Discovery 2004, 3, 935-949
- (2004) Nat. Rev. Drug Discovery , vol.3 , pp. 935-949
- Kitchen, D.B.¹ Decornez, H.² Furr, J.R.³ Bajorath, J.⁴

3
- 33749021099
- Czodrowski, P.; Dramburg, I.; Sotriffer, C. A.; Klebe, G. Proteins: Struct., Funct., Bioinf. 2006, 65, 424-437
- (2006) Proteins: Struct., Funct., Bioinf. , vol.65 , pp. 424-437
- Czodrowski, P.¹ Dramburg, I.² Sotriffer, C.A.³ Klebe, G.⁴

4
- 0032586776
- Lamotte-Brasseur, J.; Lounnas, V.; Raquet, X.; Wade, R. C. Protein Sci. 1999, 8, 404-409
- (1999) Protein Sci. , vol.8 , pp. 404-409
- Lamotte-Brasseur, J.¹ Lounnas, V.² Raquet, X.³ Wade, R.C.⁴

5
- 57349090665
- Bas, D. C.; Rogers, D. M.; Jensen, J. H. Proteins: Struct., Funct., Bioinf. 2008, 73, 765-783
- (2008) Proteins: Struct., Funct., Bioinf. , vol.73 , pp. 765-783
- Bas, D.C.¹ Rogers, D.M.² Jensen, J.H.³

6
- 77749292431
- Aguilar, B.; Anandakrishnan, R.; Ruscio, J. Z.; Onufriev, A. V. Biophys. J. 2010, 98, 872-880
- (2010) Biophys. J. , vol.98 , pp. 872-880
- Aguilar, B.¹ Anandakrishnan, R.² Ruscio, J.Z.³ Onufriev, A.V.⁴

7
- 79951476387
- Olsson, M. H.; Søndergard, C. R.; Rostkowski, M.; Jensen, J. H. J. Chem. Theory Comput. 2011, 7, 525-537
- (2011) J. Chem. Theory Comput. , vol.7 , pp. 525-537
- Olsson, M.H.¹ Søndergard, C.R.² Rostkowski, M.³ Jensen, J.H.⁴

8
- 28644432877
- Li, H.; Robertson, A. D.; Jensen, J. H. Proteins: Struct., Funct., Bioinf. 2005, 61, 704-721
- (2005) Proteins: Struct., Funct., Bioinf. , vol.61 , pp. 704-721
- Li, H.¹ Robertson, A.D.² Jensen, J.H.³

9
- 33745099338
- Klingen, A. R.; Bombarda, E.; Ullmann, G. M. Photochem. Photobiol. Sci. 2006, 5, 588-596
- (2006) Photochem. Photobiol. Sci. , vol.5 , pp. 588-596
- Klingen, A.R.¹ Bombarda, E.² Ullmann, G.M.³

10
- 38048998514
- Søndergaard, C. R.; McIntosh, L. P.; Pollastri, G.; Nielsen, J. E. J. Mol. Biol. 2008, 376, 269-287
- (2008) J. Mol. Biol. , vol.376 , pp. 269-287
- Søndergaard, C.R.¹ McIntosh, L.P.² Pollastri, G.³ Nielsen, J.E.⁴

11
- 0029666454
- McIntosh, L. P.; Hand, G.; Johnson, P. E.; Joshi, M. D.; Korner, M.; Plesniak, L. A.; Ziser, L.; Wakarchuk, W. W.; Withers, S. G. Biochemistry 1996, 35, 9958-9966
- (1996) Biochemistry , vol.35 , pp. 9958-9966
- McIntosh, L.P.¹ Hand, G.² Johnson, P.E.³ Joshi, M.D.⁴ Korner, M.⁵ Plesniak, L.A.⁶ Ziser, L.⁷ Wakarchuk, W.W.⁸ Withers, S.G.⁹

12
- 0030023620
- Qin, J.; Clore, G. M.; Gronenborn, A. M. Biochemistry 1996, 35, 7-13
- (1996) Biochemistry , vol.35 , pp. 7-13
- Qin, J.¹ Clore, G.M.² Gronenborn, A.M.³

13
- 0030608830
- Chivers, P. T.; Prehoda, K. E.; Volkman, B. F.; Kim, B.-M.; Markley, J. L.; Raines, R. T. Biochemistry 1997, 36, 14985-14991
- (1997) Biochemistry , vol.36 , pp. 14985-14991
- Chivers, P.T.¹ Prehoda, K.E.² Volkman, B.F.³ Kim, B.-M.⁴ Markley, J.L.⁵ Raines, R.T.⁶

14
- 0029057023
- Jeng, M.; Holmgren, A.; Dyson, H. Biochemistry 1995, 34, 10101-10105
- (1995) Biochemistry , vol.34 , pp. 10101-10105
- Jeng, M.¹ Holmgren, A.² Dyson, H.³

15
- 18844363229
- accessed Feb 14, 2009
- van Rossum, G. The Python Language Reference (accessed Feb 14, 2009); http://docs.python.org/py3k/reference/index.html.
- The Python Language Reference
- Van Rossum, G.¹

16
- 84978813676
- a Data Compiled by R. Williams; research.chem.psu.edu/brpgroup/pKa-compilation.pdf.
- A Data Compiled by R. Williams
- Williams, R.¹

17
- 79960220046
- Functional Groups
- CRC Press: Boca Raton, FL
- Smith, M. Functional Groups. Organic Chemistry: An Acid-Base Approach; CRC Press: Boca Raton, FL, 2011; p 142.
- (2011) Organic Chemistry: An Acid-Base Approach , pp. 142
- Smith, M.¹

18
- 0019889036
- Warshel, A. Biochemistry 1981, 20, 3167-3177
- (1981) Biochemistry , vol.20 , pp. 3167-3177
- Warshel, A.¹

19
- 79960232629
- ChemAxon, (accessed Jan 15, 2010)
- ChemAxon, MarvinSketch 5.2.6 (accessed Jan 15, 2010), 2009; http://www.chemaxon.com/products/marvin/marvinsketch/.
- (2009) MarvinSketch 5.2.6

20
- 37749011993
- Shelley, J. C.; Cholleti, A.; Frye, L. L.; Greenwood, J. R.; Timlin, M. R.; Uchimaya, M. J. Comput.-Aided Mol. Des. 2007, 21, 681-691
- (2007) J. Comput.-Aided Mol. Des. , vol.21 , pp. 681-691
- Shelley, J.C.¹ Cholleti, A.² Frye, L.L.³ Greenwood, J.R.⁴ Timlin, M.R.⁵ Uchimaya, M.⁶

21
- 0033954256
- Berman, H.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.; Weissig, H.; Shindyalov, I.; Bourne, P. Nucleic Acids Res. 2000, 28, 235-242
- (2000) Nucleic Acids Res. , vol.28 , pp. 235-242
- Berman, H.¹ Westbrook, J.² Feng, Z.³ Gilliland, G.⁴ Bhat, T.⁵ Weissig, H.⁶ Shindyalov, I.⁷ Bourne, P.⁸

22
- 3142708566
- Alexov, E. Proteins: Struct., Funct., Bioinf. 2004, 56, 572-584
- (2004) Proteins: Struct., Funct., Bioinf. , vol.56 , pp. 572-584
- Alexov, E.¹

23
- 0025398721
- Vriend, G. J. Mol. Graphics 1990, 8, 52-56
- (1990) J. Mol. Graphics , vol.8 , pp. 52-56
- Vriend, G.¹

24
- 0035955550
- Dullweber, F.; Stubbs, M. T.; Musil, D.; Stürzebecher, J.; Klebe, G. J. Mol. Biol. 2001, 313, 593-614
- (2001) J. Mol. Biol. , vol.313 , pp. 593-614
- Dullweber, F.¹ Stubbs, M.T.² Musil, D.³ Stürzebecher, J.⁴ Klebe, G.⁵

25
- 0029878720
- Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33-38
- (1996) J. Mol. Graphics , vol.14 , pp. 33-38
- Humphrey, W.¹ Dalke, A.² Schulten, K.³

26
- 79251535315
- Rostkowski, M.; Olsson, M.; Søndergaard, C.; Jensen, J. H. BMC Struct. Biol. 2011, 11, 6
- (2011) BMC Struct. Biol. , vol.11 , pp. 6
- Rostkowski, M.¹ Olsson, M.² Søndergaard, C.³ Jensen, J.H.⁴

27
- 0033815251
- Velazquez-Campoy, A.; Luque, I.; Todd, M. J.; Milutinovich, M.; Kiso, Y.; Freire, E. Protein Sci. 2000, 9, 1801-1809
- (2000) Protein Sci. , vol.9 , pp. 1801-1809
- Velazquez-Campoy, A.¹ Luque, I.² Todd, M.J.³ Milutinovich, M.⁴ Kiso, Y.⁵ Freire, E.⁶

28
- 79960283880
- The Diazines: Pyridazine, Pyrimidine, and Pyrazine: Reactions and Synthesis
- 5 th ed.; Wiley-Blackwell: Chichester, UK
- Joule, J. A.; Mills, K. The Diazines: Pyridazine, Pyrimidine, and Pyrazine: Reactions and Synthesis. Heterocyclic Chemistry, 5 th ed.; Wiley-Blackwell: Chichester, UK, 2010; p 254.
- (2010) Heterocyclic Chemistry , pp. 254
- Joule, J.A.¹ Mills, K.²

29
- 12344318177
- Hartshorn, M. J.; Murray, C. W.; Cleasby, A.; Frederickson, M.; Tickle, I. J.; Jhoti, H. J. Med. Chem. 2005, 48, 403-413
- (2005) J. Med. Chem. , vol.48 , pp. 403-413
- Hartshorn, M.J.¹ Murray, C.W.² Cleasby, A.³ Frederickson, M.⁴ Tickle, I.J.⁵ Jhoti, H.⁶

30
- 0031308324
- Tari, L.; Matte, A.; Goldie, H.; Delbaere, L. Nat. Struct. Biol. 1997, 4, 990-994
- (1997) Nat. Struct. Biol. , vol.4 , pp. 990-994
- Tari, L.¹ Matte, A.² Goldie, H.³ Delbaere, L.⁴

31
- 33947119575
- Czodrowski, P.; Sotriffer, C. A.; Klebe, G. J. Mol. Biol. 2007, 367, 1347-1356
- (2007) J. Mol. Biol. , vol.367 , pp. 1347-1356
- Czodrowski, P.¹ Sotriffer, C.A.² Klebe, G.³

32
- 32044460444
- Fokkens, J.; Klebe, G. Angew. Chem., Int. Ed. 2006, 45, 985-989
- (2006) Angew. Chem., Int. Ed. , vol.45 , pp. 985-989
- Fokkens, J.¹ Klebe, G.²

33
- 0032924352
- Bernstein, N. K.; Cherney, M. M.; Loetscher, H.; Ridley, R. G.; James, M. N. Nat. Struct. Mol. Biol. 1999, 6, 32-37
- (1999) Nat. Struct. Mol. Biol. , vol.6 , pp. 32-37
- Bernstein, N.K.¹ Cherney, M.M.² Loetscher, H.³ Ridley, R.G.⁴ James, M.N.⁵

34
- 16044374702
- Silva, A. M.; Lee, A. Y.; Gulnik, S. V.; Maier, P.; Collins, J.; Bhat, T. N.; Collins, P. J.; Cachau, R. E.; Luker, K. E.; Gluzman, I. Y.; Francis, S. E.; Oksman, A.; Goldberg, D. E.; Erickson, J. W. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 10034-10039
- (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 10034-10039
- Silva, A.M.¹ Lee, A.Y.² Gulnik, S.V.³ Maier, P.⁴ Collins, J.⁵ Bhat, T.N.⁶ Collins, P.J.⁷ Cachau, R.E.⁸ Luker, K.E.⁹ Gluzman, I.Y.¹⁰ Francis, S.E.¹¹ Oksman, A.¹² Goldberg, D.E.¹³ Erickson, J.W.¹⁴

35
- 0031670902
- Lee, A. Y.; Gulnik, S. V.; Erickson, J. W. Nat. Struct. Mol. Biol. 1998, 5, 866-871
- (1998) Nat. Struct. Mol. Biol. , vol.5 , pp. 866-871
- Lee, A.Y.¹ Gulnik, S.V.² Erickson, J.W.³

36
- 0027165319
- Baldwin, E. T.; Bhat, T. N.; Gulnik, S.; Hosur, M. V.; Sowder, R. C.; Cachau, R. E.; Collins, J.; Silva, A. M.; Erickson, J. W. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 6796-6800
- (1993) Proc. Natl. Acad. Sci. U.S.A. , vol.90 , pp. 6796-6800
- Baldwin, E.T.¹ Bhat, T.N.² Gulnik, S.³ Hosur, M.V.⁴ Sowder, R.C.⁵ Cachau, R.E.⁶ Collins, J.⁷ Silva, A.M.⁸ Erickson, J.W.⁹

37
- 0021767550
- Pearl, L.; Blundell, T. FEBS Lett. 1984, 174, 96-101
- (1984) FEBS Lett. , vol.174 , pp. 96-101
- Pearl, L.¹ Blundell, T.²

38
- 0025108755
- Fitzgerald, P. M.; McKeever, B. M.; VanMiddlesworth, J. F.; Springer, J. P.; Heimbach, J. C.; Leu, C. T.; Herber, W. K.; Dixon, R. A.; Darke, P. L. J. Biol. Chem. 1990, 265, 14209-14219
- (1990) J. Biol. Chem. , vol.265 , pp. 14209-14219
- Fitzgerald, P.M.¹ McKeever, B.M.² Vanmiddlesworth, J.F.³ Springer, J.P.⁴ Heimbach, J.C.⁵ Leu, C.T.⁶ Herber, W.K.⁷ Dixon, R.A.⁸ Darke, P.L.⁹

39
- 0026344399
- Spinelli, S.; Liu, Q.; Alzari, P.; Hirel, P.; Poljak, R. Biochimie 1991, 73, 1391-1396
- (1991) Biochimie , vol.73 , pp. 1391-1396
- Spinelli, S.¹ Liu, Q.² Alzari, P.³ Hirel, P.⁴ Poljak, R.⁵

40
- 0024412506
- Wlodawer, A.; Miller, M.; Jaskólski, M.; Sathyanarayana, B.; Baldwin, E.; Weber, I.; Selk, L.; Clawson, L.; Schneider, J.; Kent, S. Science 1989, 245, 616-21
- (1989) Science , vol.245 , pp. 616-21
- Wlodawer, A.¹ Miller, M.² Jaskólski, M.³ Sathyanarayana, B.⁴ Baldwin, E.⁵ Weber, I.⁶ Selk, L.⁷ Clawson, L.⁸ Schneider, J.⁹ Kent, S.¹⁰

41
- 0029644939
- Baldwin, E.; Bhat, T.; Gulnik, S.; Liu, B.; Topol, I.; Kiso, Y.; Mimoto, T.; Mitsuya, H.; Erickson, J. Structure 1995, 3, 581-590
- (1995) Structure , vol.3 , pp. 581-590
- Baldwin, E.¹ Bhat, T.² Gulnik, S.³ Liu, B.⁴ Topol, I.⁵ Kiso, Y.⁶ Mimoto, T.⁷ Mitsuya, H.⁸ Erickson, J.⁹

42
- 9544235162
- Lam, P. Y. S. J. Med. Chem. 1996, 39, 3514-3525
- (1996) J. Med. Chem. , vol.39 , pp. 3514-3525
- Lam, P.Y.S.¹

43
- 0025002985
- Brady, K.; Wei, A.; Ringe, D.; Abeles, R. Biochemistry 1990, 29, 7600-7607
- (1990) Biochemistry , vol.29 , pp. 7600-7607
- Brady, K.¹ Wei, A.² Ringe, D.³ Abeles, R.⁴

44
- 0033609135
- Sidhu, G.; Withers, S.; Nguyen, N.; McIntosh, L.; Ziser, L.; Brayer, G. Biochemistry 1999, 38, 5346-5354
- (1999) Biochemistry , vol.38 , pp. 5346-5354
- Sidhu, G.¹ Withers, S.² Nguyen, N.³ McIntosh, L.⁴ Ziser, L.⁵ Brayer, G.⁶

45
- 0344223475
- Sun, Z.; Dotsch, V.; Kim, M.; Li, J.; Reinherz, E.; Wagner, G. EMBO J. 1999, 18, 2941-2949
- (1999) EMBO J. , vol.18 , pp. 2941-2949
- Sun, Z.¹ Dotsch, V.² Kim, M.³ Li, J.⁴ Reinherz, E.⁵ Wagner, G.⁶

46
- 0032852375
- Zuegg, J.; Gruber, K.; Gugganig, M.; Wagner, U.; Kratky, C. Protein Sci. 1999, 8, 1990-2000
- (1999) Protein Sci. , vol.8 , pp. 1990-2000
- Zuegg, J.¹ Gruber, K.² Gugganig, M.³ Wagner, U.⁴ Kratky, C.⁵

47
- 0020441466
- Bolin, J.; Filman, D.; Matthews, D.; Hamlin, R.; Kraut, J. J. Biol. Chem. 1982, 257, 13650-13662
- (1982) J. Biol. Chem. , vol.257 , pp. 13650-13662
- Bolin, J.¹ Filman, D.² Matthews, D.³ Hamlin, R.⁴ Kraut, J.⁵

48
- 0029859529
- Smith, R.; Brereton, I. M.; Chai, R. Y.; Kent, S. B. Nat. Struct. Mol. Biol. 1996, 3, 946-950
- (1996) Nat. Struct. Mol. Biol. , vol.3 , pp. 946-950
- Smith, R.¹ Brereton, I.M.² Chai, R.Y.³ Kent, S.B.⁴

49
- 0028114966
- Yamazaki, T.; Nicholson, L. K.; Wingfield, P.; Stahl, S. J.; Kaufman, J. D.; Eyermann, C. J.; Hodge, C. N.; Lam, P. Y. S.; Torchia, D. A. J. Am. Chem. Soc. 1994, 116, 10791-10792
- (1994) J. Am. Chem. Soc. , vol.116 , pp. 10791-10792
- Yamazaki, T.¹ Nicholson, L.K.² Wingfield, P.³ Stahl, S.J.⁴ Kaufman, J.D.⁵ Eyermann, C.J.⁶ Hodge, C.N.⁷ Lam, P.Y.S.⁸ Torchia, D.A.⁹

50
- 0942298096
- Stranzl, G. R.; Gruber, K.; Steinkellner, G.; Zangger, K.; Schwab, H.; Kratky, C. J. Biol. Chem. 2004, 279, 3699-3707
- (2004) J. Biol. Chem. , vol.279 , pp. 3699-3707
- Stranzl, G.R.¹ Gruber, K.² Steinkellner, G.³ Zangger, K.⁴ Schwab, H.⁵ Kratky, C.⁶

51
- 0019490836
- Cocco, L.; Groff, J. P.; Temple, C.; Montgomery, J. A.; London, R. E.; Matwiyoff, N. A.; Blakley, R. L. Biochemistry 1981, 20, 3972-3978
- (1981) Biochemistry , vol.20 , pp. 3972-3978
- Cocco, L.¹ Groff, J.P.² Temple, C.³ Montgomery, J.A.⁴ London, R.E.⁵ Matwiyoff, N.A.⁶ Blakley, R.L.⁷

52
- 0020591068
- Cocco, L.; Roth, B.; Temple, C.; Montgomery, J. A.; London, R. E.; Blakley, R. L. Arch. Biochem. Biophys. 1983, 226, 567-577
- (1983) Arch. Biochem. Biophys. , vol.226 , pp. 567-577
- Cocco, L.¹ Roth, B.² Temple, C.³ Montgomery, J.A.⁴ London, R.E.⁵ Blakley, R.L.⁶

53
- 0020619163
- Stone, S.; Morrison, J. Biochim. Biophys. Acta 1983, 745, 247-258
- (1983) Biochim. Biophys. Acta , vol.745 , pp. 247-258
- Stone, S.¹ Morrison, J.²

54
- 0023036722
- London, R.; Howell, E.; Warren, M.; Kraut, J.; Blakley, R. Biochemistry 1986, 25, 7229-7235
- (1986) Biochemistry , vol.25 , pp. 7229-7235
- London, R.¹ Howell, E.² Warren, M.³ Kraut, J.⁴ Blakley, R.⁵

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.