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Journal of Chemical Theory and Computation

Volumn 3, Issue 3, 2007, Pages 1193-1202

Rapid, accurate, and precise calculation of relative binding affinities for the SH2 domain using a computational grid

(5) Fowler, Philip W a Geroult, Sebastien b Jha, Shantenu a Waksman, Gabriel a,b Coveney, Peter V a

a UNIVERSITY COLLEGE LONDON (United Kingdom)

b UNIVERSITY OF LONDON (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 36148944514 PISSN: 15499618 EISSN: None Source Type: Journal
DOI: 10.1021/ct6003017 Document Type: Article

Times cited : (13)

References (76)

1
- 0028155689
- Åqvist, J.; Medina, C.; Samuelsson, J.-E. Protein. Eng. 1994, 7, 385-391.
- (1994) Protein. Eng , vol.7 , pp. 385-391
- Åqvist, J.¹ Medina, C.² Samuelsson, J.-E.³

2
- 4244116139
- Jarzynski, C. Phys. Rev. E 1997, 56, 5018-5035.
- (1997) Phys. Rev. E , vol.56 , pp. 5018-5035
- Jarzynski, C.¹

3
- 3042688939
- Ytreberg, F. M.; Zuckerman, D. M. J. Chem. Phys. 2004, 120, 10876-10879.
- (2004) J. Chem. Phys , vol.120 , pp. 10876-10879
- Ytreberg, F.M.¹ Zuckerman, D.M.²

4
- 0032560959
- Srinivasan, J.; Cheatham, T. E., III; Cieplak, P.; Kollman, P. A.; Case, D. A. J. Am. Chem. Soc. 1998, 120, 9401-9409.
- (1998) J. Am. Chem. Soc , vol.120 , pp. 9401-9409
- Srinivasan, J.¹ Cheatham III, T.E.² Cieplak, P.³ Kollman, P.A.⁴ Case, D.A.⁵

5
- 0031872292
- Vorobjev, Y. N.; Almagro, J. C.; Hermans, J. Proteins 1998, 32, 399-413.
- (1998) Proteins , vol.32 , pp. 399-413
- Vorobjev, Y.N.¹ Almagro, J.C.² Hermans, J.³

6
- 33646178918
- Lee, M. S.; Olson, M. A. Biophys. J. 2006, 90, 864-877.
- (2006) Biophys. J , vol.90 , pp. 864-877
- Lee, M.S.¹ Olson, M.A.²

7
- 0035960174
- Damodaran, K. V.; Banba, S.; Brooks, C. L., III J. Phys. Chem. B 2001, 105, 9316-9322.
- (2001) J. Phys. Chem. B , vol.105 , pp. 9316-9322
- Damodaran, K.V.¹ Banba, S.² Brooks III, C.L.³

8
- 4344660645
- Hénin, J.; Chipot, C. J. Chem. Phys. 2004, 121, 2904-3004.
- (2004) J. Chem. Phys , vol.121 , pp. 2904-3004
- Hénin, J.¹ Chipot, C.²

9
- 23744508332
- Rodinger, T.; Howell, P. L.; Pomès, R. J. Chem. Phys. 2005, 123, 034104.
- (2005) J. Chem. Phys , vol.123 , pp. 034104
- Rodinger, T.¹ Howell, P.L.² Pomès, R.³

10
- 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

11
- 33846202602
- Rodinger, T.; Howell, P. L.; Pomès, R. J. Chem. Theor. Comput. 2006, 2, 725-731.
- (2006) J. Chem. Theor. Comput , vol.2 , pp. 725-731
- Rodinger, T.¹ Howell, P.L.² Pomès, R.³

12
- 33846264022
- Rick, S. W. J. Chem. Theor. Comput. 2006, 2, 939-946.
- (2006) J. Chem. Theor. Comput , vol.2 , pp. 939-946
- Rick, S.W.¹

13
- 0037440856
- Lu, N.; Singh, J. K.; Kofke, D. A. J. Chem. Phys. 2003, 118, 2977-2984.
- (2003) J. Chem. Phys , vol.118 , pp. 2977-2984
- Lu, N.¹ Singh, J.K.² Kofke, D.A.³

14
- 23944432199
- Shirts, M. R.; Pande, V. S. J. Chem. Phys. 2005, 122, 144107.
- (2005) J. Chem. Phys , vol.122 , pp. 144107
- Shirts, M.R.¹ Pande, V.S.²

15
- 1542742143
- Yang, W.; Bitetti-Putzer, R.; Karplus, M. J. Chem. Phys. 2004, 120, 2618-2628.
- (2004) J. Chem. Phys , vol.120 , pp. 2618-2628
- Yang, W.¹ Bitetti-Putzer, R.² Karplus, M.³

16
- 17044382128
- Rodinger, T.; Pomès, R. Curr. Opin. Struct. Biol. 2005, 15, 164-170.
- (2005) Curr. Opin. Struct. Biol , vol.15 , pp. 164-170
- Rodinger, T.¹ Pomès, R.²

17
- 17544366862
- Kofke, D. A. Fluid Phase Equilib. 2005, 228-229, 41-48.
- (2005) Fluid Phase Equilib , vol.228-229 , pp. 41-48
- Kofke, D.A.¹

18
- 33646943202
- Adcock, S. A.; McCammon, J. A. Chem. Rev. 2006, 106, 1589-1615.
- (2006) Chem. Rev , vol.106 , pp. 1589-1615
- Adcock, S.A.¹ McCammon, J.A.²

19
- 36148947062
- Rodriguez-Gomez, D.; Garve, E.; Pohorille, A. J. Chem. Phys. 2004, 120, 2563-2578.
- (2004) J. Chem. Phys , vol.120 , pp. 2563-2578
- Rodriguez-Gomez, D.¹ Garve, E.² Pohorille, A.³

20
- 33750970530
- Ytreberg, F. M.; Swendsen, R. H.; Zuckerman, D. M. J. Chem. Phys. 2006, 125, 184114.
- (2006) J. Chem. Phys , vol.125 , pp. 184114
- Ytreberg, F.M.¹ Swendsen, R.H.² Zuckerman, D.M.³

21
- 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

22
- 25144498041
- Fowler, P. W.; Jha, S.; Coveney, P. V. Philos. Trans. R. Soc. London, Ser. A 2005, 363, 1999-2015.
- (2005) Philos. Trans. R. Soc. London, Ser. A , vol.363 , pp. 1999-2015
- Fowler, P.W.¹ Jha, S.² Coveney, P.V.³

23
- 12844283323
- Machida, K.; Mayer, B. J. Biochim. Biophys. Acta 2005, 1747, 1-25.
- (2005) Biochim. Biophys. Acta , vol.1747 , pp. 1-25
- Machida, K.¹ Mayer, B.J.²

24
- 0037453510
- Pawson, T.; Nash, P. Science 2003, 300, 445-452.
- (2003) Science , vol.300 , pp. 445-452
- Pawson, T.¹ Nash, P.²

25
- 0035895505
- Venter, J. C. et al. Science 2001, 291, 1304-1352.
- (2001) Science , vol.291 , pp. 1304-1352
- Venter, J.C.¹

26
- 31044448846
- Waksman, G.; Kumaran, S.; Lubman, O. Expert Rev. Mol. Med. 2004, 6, 1-18.
- (2004) Expert Rev. Mol. Med , vol.6 , pp. 1-18
- Waksman, G.¹ Kumaran, S.² Lubman, O.³

27
- 0035415663
- Shakespeare, W. C. Curr. Opin. Chem. Biol. 2001, 5, 409-415.
- (2001) Curr. Opin. Chem. Biol , vol.5 , pp. 409-415
- Shakespeare, W.C.¹

28
- 0027409064
- Waksman, G.; Shoelson, S. E.; Pant, N.; Cowburn, D.; Kuriyan, J. Cell 1993, 72, 779-790.
- (1993) Cell , vol.72 , pp. 779-790
- Waksman, G.¹ Shoelson, S.E.² Pant, N.³ Cowburn, D.⁴ Kuriyan, J.⁵

29
- 0026698924
- Waksman, G.; Kominos, D.; Robertson, S. C.; Pant, N.; Baltimore, D.; Birge, R. B.; Cowburn, D.; Hanafusa, H.; Mayer, B. J.; Overduin, M.; Resh, M. D.; Rios, C. B.; Silverman, L.; Kuriyan, J. Nature 1992, 358, 646-653.
- (1992) Nature , vol.358 , pp. 646-653
- Waksman, G.¹ Kominos, D.² Robertson, S.C.³ Pant, N.⁴ Baltimore, D.⁵ Birge, R.B.⁶ Cowburn, D.⁷ Hanafusa, H.⁸ Mayer, B.J.⁹ Overduin, M.¹⁰ Resh, M.D.¹¹ Rios, C.B.¹² Silverman, L.¹³ Kuriyan, J.¹⁴

30
- 0027403027
- Songyang, Z. et al. Cell 1993, 72, 767-778.
- (1993) Cell , vol.72 , pp. 767-778
- Songyang, Z.¹

31
- 0027502504
- Eck, M. J.; Shoelson, S. E.; Harrison, S. C. Nature 1993, 362, 87-91.
- (1993) Nature , vol.362 , pp. 87-91
- Eck, M.J.¹ Shoelson, S.E.² Harrison, S.C.³

32
- 0033527682
- Bradshaw, J. M.; Mitaxov, V.; Waksman, G. J. Mol. Biol. 1999, 293, 971-985.
- (1999) J. Mol. Biol , vol.293 , pp. 971-985
- Bradshaw, J.M.¹ Mitaxov, V.² Waksman, G.³

33
- 0033586726
- Bradshaw, J. M.; Waksman, G. Biochemistry 1999, 38, 5147-5154.
- (1999) Biochemistry , vol.38 , pp. 5147-5154
- Bradshaw, J.M.¹ Waksman, G.²

34
- 0032560622
- Bradshaw, J. M.; Grucza, R. A.; Ladbury, J. E.; Waksman, G. Biochemistry 1998, 37, 9083-9090.
- (1998) Biochemistry , vol.37 , pp. 9083-9090
- Bradshaw, J.M.¹ Grucza, R.A.² Ladbury, J.E.³ Waksman, G.⁴

35
- 10844229225
- Wan, S.; Stote, R.; Karplus, M. J. Chem. Phys. 2004, 121, 9539.
- (2004) J. Chem. Phys , vol.121 , pp. 9539
- Wan, S.¹ Stote, R.² Karplus, M.³

36
- 0000008625
- Free energy calculations: Methods and Applications
- Schleyer, P. v. R, Ed, Wiley: Chichester
- Pearlman, D. A.; Rao, B. G. Free energy calculations: Methods and Applications. In Encyclopedia of Computational Chemistry; Schleyer, P. v. R., Ed.; Wiley: Chichester, 1999; Vol. 2, pp 1036-1061.
- (1999) Encyclopedia of Computational Chemistry , vol.2 , pp. 1036-1061
- Pearlman, D.A.¹ Rao, B.G.²

37
- 0033778163
- Henriques, D. A.; Ladbury, J. E.; Jackson, R. M. Protein Sci. 2000, 9, 1975-1985.
- (2000) Protein Sci , vol.9 , pp. 1975-1985
- Henriques, D.A.¹ Ladbury, J.E.² Jackson, R.M.³

38
- 33745066058
- Geroult, S.; Virdee, S.; Waksman, G. Chem. Biol. Drug Des. 2006, 67, 38-45.
- (2006) Chem. Biol. Drug Des , vol.67 , pp. 38-45
- Geroult, S.¹ Virdee, S.² Waksman, G.³

39
- 0034749820
- Price, D. L.; Jorgensen, W. L. J. Comput.-Aided Mol. Des. 2001, 15, 681-695.
- (2001) J. Comput.-Aided Mol. Des , vol.15 , pp. 681-695
- Price, D.L.¹ Jorgensen, W.L.²

40
- 0038219754
- Suenaga, A.; Hatakeyama, M.; Ichikawa, M.; Yu, X.; Futatsugi, N.; Narumi, T.; Fukui, K.; Terada, T.; Taiji, M.; Shirouzu, M.; Yokoyama, S.; Konagaya, A. Biochemistry 2003, 42, 5195-5200.
- (2003) Biochemistry , vol.42 , pp. 5195-5200
- Suenaga, A.¹ Hatakeyama, M.² Ichikawa, M.³ Yu, X.⁴ Futatsugi, N.⁵ Narumi, T.⁶ Fukui, K.⁷ Terada, T.⁸ Taiji, M.⁹ Shirouzu, M.¹⁰ Yokoyama, S.¹¹ Konagaya, A.¹²

41
- 0942266531
- Donnini, S.; Juffer, A. J. Comput. Chem. 2003, 25, 393-411.
- (2003) J. Comput. Chem , vol.25 , pp. 393-411
- Donnini, S.¹ Juffer, A.²

42
- 18744372751
- Woo, H.-J.; Roux, B. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6825-6830.
- (2005) Proc. Natl. Acad. Sci. U.S.A , vol.102 , pp. 6825-6830
- Woo, H.-J.¹ Roux, B.²

43
- 33646471468
- Kirkwood, J. G. J. Chem. Phys. 1935, 3, 300-313.
- (1935) J. Chem. Phys , vol.3 , pp. 300-313
- Kirkwood, J.G.¹

44
- 1542531903
- Peter, C.; Oostenbrink, C.; van Dorp, A.; van Gunsteren, W. F. J. Chem. Phys. 2004, 120, 2652-2661.
- (2004) J. Chem. Phys , vol.120 , pp. 2652-2661
- Peter, C.¹ Oostenbrink, C.² van Dorp, A.³ van Gunsteren, W.F.⁴

45
- 0028334097
- Mark, A. E.; van Gunsteren, W. F. J. Mol. Biol. 1994, 240, 167-176.
- (1994) J. Mol. Biol , vol.240 , pp. 167-176
- Mark, A.E.¹ van Gunsteren, W.F.²

46
- 22544467432
- Wan, S.; Coveney, P. V.; Flower, D. R. J. Immunology 2005, 175, 1715-1723.
- (2005) J. Immunology , vol.175 , pp. 1715-1723
- Wan, S.¹ Coveney, P.V.² Flower, D.R.³

47
- 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

48
- 0027968902
- Boresch, S.; Archontis, G.; Karplus, M. Proteins: Struct., Funct., Genet. 1994, 20, 25-33.
- (1994) Proteins: Struct., Funct., Genet , vol.20 , pp. 25-33
- Boresch, S.¹ Archontis, G.² Karplus, M.³

49
- 0035455653
- Foster, I.; Kesselman, C.; Tuecke, S. Int. J. Supercomput. Appl. 2001, 15, 200-224.
- (2001) Int. J. Supercomput. Appl , vol.15 , pp. 200-224
- Foster, I.¹ Kesselman, C.² Tuecke, S.³

50
- 33044506498
- Coveney, P. V.; Fowler, P. W. J. R. Soc. Interface 2005, 2, 267-280.
- (2005) J. R. Soc. Interface , vol.2 , pp. 267-280
- Coveney, P.V.¹ Fowler, P.W.²

51
- 25144514551
- Coveney, P. V., Ed.; Scientific Grid Computing. Philos. Trans. R. Soc. London, Ser. A 2005, 363(1833), 1705-2053.
- Coveney, P. V., Ed.; Scientific Grid Computing. Philos. Trans. R. Soc. London, Ser. A 2005, 363(1833), 1705-2053.

52
- 0042415783
- Kalé, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadara, jan, K.; Schulten, K. J. Comput. Phys. 1999, 151, 283-312.
- (1999) J. Comput. Phys , vol.151 , pp. 283-312
- Kalé, L.¹ Skeel, R.² Bhandarkar, M.³ Brunner, R.⁴ Gursoy, A.⁵ Krawetz, N.⁶ Phillips, J.⁷ Shinozaki, A.⁸ Varadara⁹ jan, K.¹⁰ Schulten, K.¹¹

53
- 27344436659
- Phillips, J.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802.
- (2005) J. Comput. Chem , vol.26 , pp. 1781-1802
- Phillips, J.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

54
- 25144516750
- Pickles, S. M.; Haines, R.; Pinning, R. L.; Porter, A. R. Philos. Trans. R. Soc. London, Ser. A 2005, 363, 1843-1853.
- (2005) Philos. Trans. R. Soc. London, Ser. A , vol.363 , pp. 1843-1853
- Pickles, S.M.¹ Haines, R.² Pinning, R.L.³ Porter, A.R.⁴

55
- 84883597655
- accessed Feb 23, 2007
- RealityGrid. http://www.realitygrid.org (accessed Feb 23, 2007).
- RealityGrid

56
- 36148955712
- Alliance, accessed Feb 23, 2007
- The Globus Alliance. http://www.globus.org (accessed Feb 23, 2007).
- The Globus

57
- 25144435508
- Kalawsky, R. S.; Nee, S. P.; Holmes, I.; Coveney, P. V. Philos. Trans. R. Soc. London, Ser. A 2005, 363, 1885-1894.
- (2005) Philos. Trans. R. Soc. London, Ser. A , vol.363 , pp. 1885-1894
- Kalawsky, R.S.¹ Nee, S.P.² Holmes, I.³ Coveney, P.V.⁴

58
- 34548806882
- accessed Feb 23, 2007
- The TeraGrid. http://www.teragrid.org (accessed Feb 23, 2007).
- The TeraGrid

59
- 36148979637
- The National Grid Service, accessed Feb 23, 2007
- The National Grid Service. http://www.ngs.ac.uk (accessed Feb 23, 2007).

60
- 36149000485
- Coveney, P. V.; Jha, S.; Pickles, S. CSAR Focus 2005, 14, 16-18.
- (2005) CSAR Focus , vol.14 , pp. 16-18
- Coveney, P.V.¹ Jha, S.² Pickles, S.³

61
- 33847221488
- Coveney, P. V.; Saksena, R. S.; Zasada, S. J.; McKeown, M.; Pickles, S. Comput. Phys. Commun. 2007, 176, 406-418.
- (2007) Comput. Phys. Commun , vol.176 , pp. 406-418
- Coveney, P.V.¹ Saksena, R.S.² Zasada, S.J.³ McKeown, M.⁴ Pickles, S.⁵

62
- 36148977879
- The Open Middleware Institute, accessed Feb 23, 2007
- The Open Middleware Institute. http://www.omii.ac.uk (accessed Feb 23, 2007).

63
- 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

64
- 36148940187
- accessed Feb 23
- Hénin, J. Alchemify, an X-PLOR PSF post-processor for alchemical free energy calculations in NAMD. http://www.edam.uhp-nancy.fr/Alchemify/ (accessed Feb 23, 2007).
- (2007) Alchemify, an X-PLOR PSF post-processor for alchemical free energy calculations in NAMD
- Hénin, J.¹

65
- 0004016501
- Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
- (1983) J. Chem. Phys , vol.79 , pp. 926-935
- Jorgensen, W.L.¹ Chandrasekhar, J.² Madura, J.D.³ Impey, R.W.⁴ Klein, M.L.⁵

66
- 0041784950
- MacKerell, A. D. et al. J. Phys. Chem. B 1998, 102, 3586-3616.
- (1998) J. Phys. Chem. B , vol.102 , pp. 3586-3616
- MacKerell, A.D.¹

67
- 0029860548
- Feng, M.-H.; Philippopoulos, M.; MacKerell, A. D. J.; Lim, C. J. Am. Chem. Soc. 1996, 118, 11265-11277.
- (1996) J. Am. Chem. Soc , vol.118 , pp. 11265-11277
- Feng, M.-H.¹ Philippopoulos, M.² MacKerell, A.D.J.³ Lim, C.⁴

68
- 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

69
- 84986440341
- Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952-962.
- (1992) J. Comput. Chem , vol.13 , pp. 952-962
- Miyamoto, S.¹ Kollman, P.A.²

70
- 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

71
- 36449002336
- Zacharias, M.; Straatsma, T. P.; McCammon, J. A. J. Chem. Phys. 1994, 100, 9025-9031.
- (1994) J. Chem. Phys , vol.100 , pp. 9025-9031
- Zacharias, M.¹ Straatsma, T.P.² McCammon, J.A.³

72
- 0003399724
- 2nd ed, Academic Press: London
- Frenkel, D.; Smit, B. Understanding Molecular Simulation, 2nd ed.; Academic Press: London, 2002; p 529.
- (2002) Understanding Molecular Simulation , pp. 529
- Frenkel, D.¹ Smit, B.²

73
- 85058247876
- Bradshaw, J. M.; Mitaxov, V.; Waksman, G. J. Mol. Biol. 2000, 299, 521-535.
- (2000) J. Mol. Biol , vol.299 , pp. 521-535
- Bradshaw, J.M.¹ Mitaxov, V.² Waksman, G.³

74
- 0037414445
- Lubman, O. Y.; Waksman, G. J. Mol. Biol. 2003, 328, 655-668.
- (2003) J. Mol. Biol , vol.328 , pp. 655-668
- Lubman, O.Y.¹ Waksman, G.²

75
- 0032530724
- Chung, E.; Henriques, D. A.; Renozi, D.; Zvelebil, M.; Waksman, G.; Robinson, C. V.; Ladbury, J. E. Structure 1998, 6, 1141-1151.
- (1998) Structure , vol.6 , pp. 1141-1151
- Chung, E.¹ Henriques, D.A.² Renozi, D.³ Zvelebil, M.⁴ Waksman, G.⁵ Robinson, C.V.⁶ Ladbury, J.E.⁷

76
- 0242551544
- Sheinerman, Felix, B.; Al-Lazikani, B.; Honig, B. J. Mol. Biol. 2003, 334, 823-841.
- Sheinerman, Felix, B.; Al-Lazikani, B.; Honig, B. J. Mol. Biol. 2003, 334, 823-841.

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