SCOPUS 정보 검색 플랫폼

Journal of Chemical Theory and Computation

Volumn 3, Issue 6, 2007, Pages 2108-2119

Improved methods for side chain and loop predictions via the protein local optimization program: Variable dielectric model for implicitly improving the treatment of polarization effects

(3) Zhu, Kai a Shirts, Michael R a Friesner, Richard A a

a Howard Hughes Medical Institute (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 36649014061 PISSN: 15499618 EISSN: None Source Type: Journal
DOI: 10.1021/ct700166f Document Type: Article

Times cited : (95)

References (49)

1
- 0036310711
- Jacobson, M. P.; Friesner, R. A.; Xiang, Z.; Honig, B. J. Mol. Biol. 2002, 320, 597-608.
- (2002) J. Mol. Biol , vol.320 , pp. 597-608
- Jacobson, M.P.¹ Friesner, R.A.² Xiang, Z.³ Honig, B.⁴

2
- 1842532008
- Jacobson, M. P.; Pincus, D. L.; Rapp, C. S.; Day, T. J. F.; Honig, B.; Shaw, D. E.; Friesner, R. A. Proteins 2004, 55, 351-367.
- (2004) Proteins , vol.55 , pp. 351-367
- Jacobson, M.P.¹ Pincus, D.L.² Rapp, C.S.³ Day, T.J.F.⁴ Honig, B.⁵ Shaw, D.E.⁶ Friesner, R.A.⁷

3
- 0037038549
- Jacobson, M. P.; Kaminski, G. A.; Friesner, R. A.; Rapp, C. S. J. Phys. Chem. B 2002, 106, 11673-11680.
- (2002) J. Phys. Chem. B , vol.106 , pp. 11673-11680
- Jacobson, M.P.¹ Kaminski, G.A.² Friesner, R.A.³ Rapp, C.S.⁴

4
- 33748988479
- Zhu, K.; Pincus, D. L.; Zhao, S.; Friesner, R. A. Proteins 2006, 65, 438-452.
- (2006) Proteins , vol.65 , pp. 438-452
- Zhu, K.¹ Pincus, D.L.² Zhao, S.³ Friesner, R.A.⁴

5
- 0029912748
- Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236.
- (1996) J. Am. Chem. Soc , vol.118 , pp. 11225-11236
- Jorgensen, W.L.¹ Maxwell, D.S.² Tirado-Rives, J.³

6
- 0035913529
- Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J. J. Phys. Chem. B 2001, 105, 6474.
- (2001) J. Phys. Chem. B , vol.105 , pp. 6474
- Kaminski, G.A.¹ Friesner, R.A.² Tirado-Rives, J.³

7
- 0037089017
- Gallicchio, E.; Zhang, L. Y.; Levy, R. M. J. Comput. Chem. 2001, 23 (5), 517-529.
- (2001) J. Comput. Chem , vol.23 , Issue.5 , pp. 517-529
- Gallicchio, E.¹ Zhang, L.Y.² Levy, R.M.³

8
- 0001246294
- Ghosh, A.; Rapp, C. S.; Friesner, R. A. J. Phys. Chem. B 1998, 102, 10983-10990.
- (1998) J. Phys. Chem. B , vol.102 , pp. 10983-10990
- Ghosh, A.¹ Rapp, C.S.² Friesner, R.A.³

9
- 28644441632
- Monnigmann, M.; Floudas, C. A. Proteins 2005, 61, 748-762.
- (2005) Proteins , vol.61 , pp. 748-762
- Monnigmann, M.¹ Floudas, C.A.²

10
- 2442449534
- Rohl, C. A.; Strauss, C. E.; Chivian, D.; Baker, D. Proteins 2004, 55, 656-677.
- (2004) Proteins , vol.55 , pp. 656-677
- Rohl, C.A.¹ Strauss, C.E.² Chivian, D.³ Baker, D.⁴

11
- 0037375742
- DePristo, M. A.; de Bakker, P.; Lovell, S. C.; Blundell, T. L. Proteins 2003, 51, 41-55.
- (2003) Proteins , vol.51 , pp. 41-55
- DePristo, M.A.¹ de Bakker, P.² Lovell, S.C.³ Blundell, T.L.⁴

12
- 0037375615
- de Bakker, P.; Depristo, M. A.; Burke, D. F.; Blundell, T. L. Proteins 2003, 51, 21-40.
- (2003) Proteins , vol.51 , pp. 21-40
- de Bakker, P.¹ Depristo, M.A.² Burke, D.F.³ Blundell, T.L.⁴

13
- 0037188507
- Xiang, Z. X.; Soto, C. S.; Honig, B. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 7432-7437.
- (2002) Proc. Natl. Acad. Sci. U.S.A , vol.99 , pp. 7432-7437
- Xiang, Z.X.¹ Soto, C.S.² Honig, B.³

14
- 0033810049
- Fiser, A.; Do, R.; Sali, A. Protein Sci. 2000, 9, 1753-1773.
- (2000) Protein Sci , vol.9 , pp. 1753-1773
- Fiser, A.¹ Do, R.² Sali, A.³

15
- 0035838974
- Xiang, Z. X.; Honig, B. J. Mol. Biol. 2001, 311, 421-430.
- (2001) J. Mol. Biol , vol.311 , pp. 421-430
- Xiang, Z.X.¹ Honig, B.²

16
- 33847037100
- Xiang, Z.; Steinbach, P. J.; Jacobson, M. P.; Friesner, R. A.; Honig, B. Proteins 2007, 66 (4), 814-823.
- (2007) Proteins , vol.66 , Issue.4 , pp. 814-823
- Xiang, Z.¹ Steinbach, P.J.² Jacobson, M.P.³ Friesner, R.A.⁴ Honig, B.⁵

17
- 0027160197
- Dunbrack, R. L. J.; Karplus, M. J. Mol. Biol 1993, 230, 543-574.
- (1993) J. Mol. Biol , vol.230 , pp. 543-574
- Dunbrack, R.L.J.¹ Karplus, M.²

18
- 1842788912
- Eyal, E.; Najmanovich, R.; McConkey, B. J.; Edelman, M.; Sobolev, V. J. Comput. Chem. 2004, 25, 712-724.
- (2004) J. Comput. Chem , vol.25 , pp. 712-724
- Eyal, E.¹ Najmanovich, R.² McConkey, B.J.³ Edelman, M.⁴ Sobolev, V.⁵

19
- 0036149564
- Liang, S.; Grishin, N. V. Protein Sci. 2002, 11, 322-331.
- (2002) Protein Sci , vol.11 , pp. 322-331
- Liang, S.¹ Grishin, N.V.²

20
- 0036643430
- Desmet, J.; Spriet, J.; Lasters, I. Proteins 2002, 48 (1), 31-43.
- (2002) Proteins , vol.48 , Issue.1 , pp. 31-43
- Desmet, J.¹ Spriet, J.² Lasters, I.³

21
- 0026589733
- Desmet, J.; Maeyer, M. D.; Hazes, B.; Lasters, I. Nature 1992, 356, 539-542.
- (1992) Nature , vol.356 , pp. 539-542
- Desmet, J.¹ Maeyer, M.D.² Hazes, B.³ Lasters, I.⁴

22
- 33847034125
- Li, X.; Jacobson, M. P.; Zhu, K.; Zhao, S.; Friesner, R. A. Proteins 2007, 66, 824-837.
- (2007) Proteins , vol.66 , pp. 824-837
- Li, X.¹ Jacobson, M.P.² Zhu, K.³ Zhao, S.⁴ Friesner, R.A.⁵

23
- 36148938697
- Zhu, K.; Shirts, M. R.; Friesner, R. A.; Jacobson, M. P. J. Chem. Theory Comput 2007, 3, 640-648.
- (2007) J. Chem. Theory Comput , vol.3 , pp. 640-648
- Zhu, K.¹ Shirts, M.R.² Friesner, R.A.³ Jacobson, M.P.⁴

24
- 0035370422
- Nielsen, J. E.; Vriend, G. Proteins 2001, 43, 403-412.
- (2001) Proteins , vol.43 , pp. 403-412
- Nielsen, J.E.¹ Vriend, G.²

25
- 0027563464
- Yang, A.; Gunner, M. R.; Sampogna, R.; Sharp, K.; Honig, B. Proteins 1993, 15, 252-265.
- (1993) Proteins , vol.15 , pp. 252-265
- Yang, A.¹ Gunner, M.R.² Sampogna, R.³ Sharp, K.⁴ Honig, B.⁵

26
- 0029665693
- Antosiewicz, J.; McCammon, J. A.; Gilson, M. K. Biochemistry 1996, 35 (24), 7819-7833.
- (1996) Biochemistry , vol.35 , Issue.24 , pp. 7819-7833
- Antosiewicz, J.¹ McCammon, J.A.² Gilson, M.K.³

27
- 0035451052
- Schutz, C. N.; Warshel, A. Proteins 2001, 44 (4), 400-417.
- (2001) Proteins , vol.44 , Issue.4 , pp. 400-417
- Schutz, C.N.¹ Warshel, A.²

28
- 33748593093
- Demchuk, E.; Wade, R. C. J. Phys. Chem. 1996, 100, 17373-17387.
- (1996) J. Phys. Chem , vol.100 , pp. 17373-17387
- Demchuk, E.¹ Wade, R.C.²

29
- 0022816745
- Gilson, M. K.; Honig, B. Biopolymers 1986, 25, 2097-2119.
- (1986) Biopolymers , vol.25 , pp. 2097-2119
- Gilson, M.K.¹ Honig, B.²

30
- 0029833446
- Simonson, T.; Brooks, C. L. J. Am. Chem. Soc. 1996, 118 (35), 8452-8458.
- (1996) J. Am. Chem. Soc , vol.118 , Issue.35 , pp. 8452-8458
- Simonson, T.¹ Brooks, C.L.²

31
- 32844457567
- Sitkoff, D.; Sharp, K. A.; Honig, B. J. Phys. Chem. B 1994, 98, 1978-1988.
- (1994) J. Phys. Chem. B , vol.98 , pp. 1978-1988
- Sitkoff, D.¹ Sharp, K.A.² Honig, B.³

32
- 0346850017
- Grossfield, A.; Ren, P.; Ponder, J. W. J. Am. Chem. Soc. 2003, 125 (50), 15671-15682.
- (2003) J. Am. Chem. Soc , vol.125 , Issue.50 , pp. 15671-15682
- Grossfield, A.¹ Ren, P.² Ponder, J.W.³

33
- 0442311067
- Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A. J. Phys. Chem. A 2004, 108, 621-627.
- (2004) J. Phys. Chem. A , vol.108 , pp. 621-627
- Kaminski, G.A.¹ Stern, H.A.² Berne, B.J.³ Friesner, R.A.⁴

34
- 0036882094
- Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A.; Cao, Y. X.; Murphy, R. B.; Zhou, R.; Halgren, T. A. J. Comput. Chem. 2002, 23, 1515-1531.
- (2002) J. Comput. Chem , vol.23 , pp. 1515-1531
- Kaminski, G.A.¹ Stern, H.A.² Berne, B.J.³ Friesner, R.A.⁴ Cao, Y.X.⁵ Murphy, R.B.⁶ Zhou, R.⁷ Halgren, T.A.⁸

35
- 33746597823
- Patel, S. A.; Brooks, C. L. Mol. Simul. 2006, 32 (3-4), 231-249.
- (2006) Mol. Simul , vol.32 , Issue.3-4 , pp. 231-249
- Patel, S.A.¹ Brooks, C.L.²

36
- 0242443693
- Ponder, J. W.; Case, D. A. Adv. Prot. Chem. 2003, 66, 27-85.
- (2003) Adv. Prot. Chem , vol.66 , pp. 27-85
- Ponder, J.W.¹ Case, D.A.²

37
- 0037899660
- Ren, P.; Ponder, J. W. J. Phys. Chem. B 2003, 107, 5933-5947.
- (2003) J. Phys. Chem. B , vol.107 , pp. 5933-5947
- Ren, P.¹ Ponder, J.W.²

38
- 0000610417
- Rick, S. W.; Berne, B. J. J. Am. Chem. Soc. 1996, 118, 672-679.
- (1996) J. Am. Chem. Soc , vol.118 , pp. 672-679
- Rick, S.W.¹ Berne, B.J.²

39
- 58149211457
- Rick, S. W.; Stuart, S. J.; Bader, J. S.; Berne, B. J. J. Mol. Liq. 1995, 65-66, 31.
- (1995) J. Mol. Liq , vol.65-66 , pp. 31
- Rick, S.W.¹ Stuart, S.J.² Bader, J.S.³ Berne, B.J.⁴

40
- 36448999850
- Rick, S. W.; Stuart, S. J.; Berne, B. J. J. Chem. Phys. 1994, 101(7), 6141.
- (1994) J. Chem. Phys , vol.101 , Issue.7 , pp. 6141
- Rick, S.W.¹ Stuart, S.J.² Berne, B.J.³

41
- 0035424605
- Stern, H. A.; Rittner, F.; Berne, B. J.; Friesner, R. A. J. Chem. Phys. 2001, 115, 2237.
- (2001) J. Chem. Phys , vol.115 , pp. 2237
- Stern, H.A.¹ Rittner, F.² Berne, B.J.³ Friesner, R.A.⁴

42
- 0036890275
- Ren, P.; Ponder, J. W. J. Comput. Chem. 2002, 23 (16), 1497-1506.
- (2002) J. Comput. Chem , vol.23 , Issue.16 , pp. 1497-1506
- Ren, P.¹ Ponder, J.W.²

43
- 30444431852
- Maple, J. R.; Cao, Y. X.; Damm, W.; Halgren, T. A.; Kaminski, G. A.; Zhang, L. Y.; Friesner, R. A. J. Chem. Theory Comput. 2005, 1 (4), 694-715.
- (2005) J. Chem. Theory Comput , vol.1 , Issue.4 , pp. 694-715
- Maple, J.R.¹ Cao, Y.X.² Damm, W.³ Halgren, T.A.⁴ Kaminski, G.A.⁵ Zhang, L.Y.⁶ Friesner, R.A.⁷

44
- 34047168032
- Schnieders, M. J.; Baker, N. A.; Ren, P.; Ponder, J. W. J. Chem. Phys. 2007, 126, 124114.
- (2007) J. Chem. Phys , vol.126 , pp. 124114
- Schnieders, M.J.¹ Baker, N.A.² Ren, P.³ Ponder, J.W.⁴

45
- 2942597884
- Yu, Z.; Jacobson, M. P.; Rapp, C. S.; Friesner, R. A. J. Phys. Chem. B 2004, 108, 6643-6654.
- (2004) J. Phys. Chem. B , vol.108 , pp. 6643-6654
- Yu, Z.¹ Jacobson, M.P.² Rapp, C.S.³ Friesner, R.A.⁴

46
- 0141704162
- Zhou, R. Proteins 2003, 53, 148-161.
- (2003) Proteins , vol.53 , pp. 148-161
- Zhou, R.¹

47
- 0036789950
- Zhou, R.; Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. 2002, 99 (20), 12777-12782.
- (2002) Proc. Natl. Acad. Sci. U.S.A , vol.99 , Issue.20 , pp. 12777-12782
- Zhou, R.¹ Berne, B.J.²

48
- 3042801661
- Felts, A. K.; Harano, Y.; Gallicchio, E.; Levy, R. M. Proteins 2004, 56 (2), 310-321.
- (2004) Proteins , vol.56 , Issue.2 , pp. 310-321
- Felts, A.K.¹ Harano, Y.² Gallicchio, E.³ Levy, R.M.⁴

49
- 33745960026
- Geney, R.; Layten, M.; Gomperts, R.; Hornak, V.; Simmerling, C. J. Chem. Theory Comput. 2005, 2 (1), 115-127.
- (2005) J. Chem. Theory Comput , vol.2 , Issue.1 , pp. 115-127
- Geney, R.¹ Layten, M.² Gomperts, R.³ Hornak, V.⁴ Simmerling, C.⁵

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.