Normal mode analysis with molecular geometry restraints: Bridging molecular mechanics and elastic models

Archives of Biochemistry and Biophysics

Volumn 508, Issue 1, 2011, Pages 64-71

  Lu, Mingyang ^a   Ma, Jianpeng ^a,b  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b Rice University   (United States)

Author keywords

All atom normal modes; Coarse graining; Energy minimization; Molecular geometry restraints; Normal mode analysis; Tip effect

Indexed keywords

ANALYTICAL PARAMETERS; ARTICLE; ATOM; CRYSTAL STRUCTURE; GEOMETRY; MATHEMATICAL MODEL; MOLECULAR GEOMETRY RESTRAINT; MOLECULAR INTERACTION; NORMAL MODE ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; VALIDATION STUDY;

CARBOHYDRATES; ELASTICITY; LIGANDS; MODELS, MOLECULAR; NUCLEOTIDES; PROTEINS;

EID: 79952387635     PISSN: 00039861     EISSN: 10960384     Source Type: Journal    
DOI: 10.1016/j.abb.2010.12.031     Document Type: Article

References (50)

1. M. Levitt, C. Sander, and P.S. Stern J. Mol. Biol. 181 1985 423 447
2. J.A. McCammon, and S. Harvey Dynamics of Proteins and Nucleic Acids 1987 Cambridge University Press Cambridge
3. C.L. Brooks III, M. Karplus, and B.M. Pettitt Adv. Chem. Phys. 71 1988 1 249
4. B.R. Brooks, D. Janezic, and M. Karplus J. Comput. Chem. 16 1995 1522 1542
5. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus J. Comput. Chem. 4 1983 187 217
6. E. Neria, S. Fischer, and M. Karplus J. Chem. Phys. 105 1996 1902 1921
7. A.D. MacKerell, D. Bashford Jr., M. Bellott, R.L. Dunbrack Jr., J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, W.E. Reiher, B. Roux, M. Schlenkrich, J.C. Smith, R. Stote, J. Straub, M. Watanabe, J. JWiorkiewicz-Kuczera, D. Yin, and M. Karplus J. Phys. Chem. B102 1998 3586 3616
8. J.M. Wang, P. Cieplak, and P.A. Kollman J. Comput. Chem. 21 2000 1049 1074
9. J.W. Ponder, and D.A. Case Adv. Protein Chem. 66 2003 27 85
10. J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman, and D.A. Case J. Comput. Chem. 25 2004 1157 1174
11. D.A. Case, T.E. Cheatham 3rd, T. Darden, H. Gohlke, R. Luo, K.M. Merz Jr., A. Onufriev, C. Simmerling, B. Wang, and R.J. Woods J. Comput. Chem. 26 2005 1668 1688
12. F. Tama, F.X. Gadea, O. Marques, and Y.H. Sanejouand Proteins 41 2000 1 7
13. D. Ming, and M.E. Wall Phys. Rev. Lett. 95 2005
14. L. Zhou, and S.A. Siegelbaum Biophys. J. 94 2008 3461 3474
15. A. Korkut, and W.A. Hendrickson Proc. Natl. Acad. Sci. 106 2009 15667 15672
16. M. Lu, and J. Ma Proc. Natl. Acad. Sci. USA 105 2008 15358 15363
17. M.M. Tirion Phys. Rev. Lett. 77 1996 1905 1908
18. T. Haliloglu, I. Bahar, and B. Erman Phys. Rev. Lett. 79 1997 3090 3093
19. A.R. Atilgan, S.R. Durell, R.L. Jernigan, M.C. Demirel, O. Keskin, and I. Bahar Biophys. J. 80 2001 505 515
20. P. Doruker, R.L. Jernigan, and I. Bahar J. Comput. Chem. 23 2002 119 127
21. O. Kurkcuoglu, R.L. Jernigan, and P. Doruker QSAR Comb. Sci. 24 2005 443 448
22. K. Eom, S.C. Baek, J.H. Ahn, and S. Na J. Comput. Chem. 28 2007 1400 1410
23. D. Ming, Y. Kong, M. Lambert, Z. Huang, and J. Ma Proc. Natl. Acad. Sci. USA 99 2002 8620 8625
24. F. Tama, W. Wriggers, and C.L. Brooks J. Mol. Biol. 321 2002 297 305
25. K. Hinsen J. Comput. Chem. 21 2000 79 85
26. D.A. Kondrashov, A.W. Van Wynsberghe, R.M. Bannen, Q. Cui, and G.N. Phillips Jr. Structure 15 2007 169 177
27. E. Lyman, J. Pfaendtner, and G.A. Voth Biophys. J. 95 2008 4183 4192
28. K. Moritsugu, and J.C. Smith Biophys. J. 93 2007 3460 3469
29. H.L. Woodcock, W. Zheng, A. Ghysels, Y. Shao, J. Kong, and B.R. Brooks J. Chem. Phy. 129 2008 214109
30. W. Zheng Biophys. J. 98 2010 3025 3034
31. T.D. Romo, and A. Grossfield Proteins 79 2011 23 34
32. M. Lu, and J. Ma D.M. Leitner, J.E. Straub, Proteins: Energy, Heat and Signal Flow 2009 CRC Press 229 245
33. M. Lu, B. Poon, and J. Ma J. Chem. Theor. Comp 2 2006 464 471
34. J.N. Stember, and W. Wriggers J. Chem. Phys. 131 2009
35. R. Mendez, and U. Bastolla Phys. Rev. Lett. 104 2010 228103
36. H. Gohlke, and M.F. Thorpe Biophys. J. 91 2006 2115 2120
37. M. Lu, and J. Ma Biophys. J. 89 2005 2395 2401
38. R.E. Tuzun, D.W. Noid, and B.G. Sumpter Macromol. Theory Simul. 5 1996 771 788
39. J. Hafner, and W. Zheng J. Chem. Phys. 130 2009 194111 194117
40. K. Suhre, and Y.H. Sanejouand Nucleic Acids Res. 32 2004 W610 W614
41. A.D. Mackerell, M. Feig, and C.L. Brooks J. Comput. Chem. 25 2004 1400 1415
42. O. Guvench, S.N. Greene, G. Kamath, J.W. Brady, R.M. Venable, R.W. Pastor, and A.D. MacKerell Jr. J. Comput. Chem. 29 2008 2543 2564
43. T. Lazaridis, and M. Karplus Proteins 35 1999 133 152
44. R.L. Dunbrack Jr., and F.E. Cohen Protein Sci. 6 1997 1661 1681
45. H. Zhou, and Y. Zhou Protein Sci. 11 2002 2714 2726
46. F.Y. Ni, B.K. Poon, Q.H. Wang, and J.P. Ma Acta Crystallogr. D - Biol. Crystallogr. 65 2009 633 643
47. X.R. Chen, B.K. Poon, A. Dousis, Q.H. Wang, and J.P. Ma Structure 15 2007 955 962
48. B.K. Poon, X.R. Chen, M.Y. Lu, N.K. Vyas, F.A. Quiocho, Q.H. Wang, and J.P. Ma Proc. Natl. Acad. Sci. USA 104 2007 7869 7874
49. X. Chen, M. Lu, B.K. Poon, Q. Wang, and J. Ma Acta Crystallogr. D - Biol. Crystallogr. 65 2009 339 347
50. X. Chen, Q. Wang, F. Ni, and J. Ma Proc. Natl. Acad. Sci. USA 107 2010 11352 11357