Browse > Article
http://dx.doi.org/10.5012/bkcs.2008.29.11.2172

Protein Structure Prediction Using an Associated Memory Hamiltonian and All-Atom Molecular Dynamics Simulations  

Kwac, Ki-Jeong (Department of Chemistry and Biochemistry, University of Texas at Austin)
Wolynes, Peter G. (Department of Chemistry and Biochemistry, University of California San Diego)
Publication Information
Bulletin of the Korean Chemical Society / v.29, no.11, 2008 , pp. 2172-2182 More about this Journal
Keywords
Protein folding; Associated memory hamiltonian; Molecular dynamics; Protein structure prediction
Citations & Related Records

Times Cited By Web Of Science : 1  (Related Records In Web of Science)
Times Cited By SCOPUS : 1
연도 인용수 순위
  • Reference
1 The definitions of the ${\alpha}R$, $\beta$, $P_{II}$, and ${\alpha}$L regions in the Ramachandran plot are the same as in the following paper: Kwac, K.; Lee, K.-K.; Han, J. B.; Oh, K.-I.; Cho, M. J. Chem. Phys. 2008, 128, 105106   DOI   ScienceOn
2 Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684   DOI
3 Garcia, A. E.; Sanbonmatsu, K. Y. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2782   DOI   ScienceOn
4 Case, D A.; Darden, T. A.; Cheatham III, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, Jr., K. M.; Pearlman, D. A.; Crowley, M.; Walker, R. C.; Zhang, W.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Wong, K. F.; Paesani, F.; Wu, X.; Brozell, S.; Tsui, V.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Mathews, D. H.; Schafmeister, C.; Ross, W. S.; Kollman, P. A. AMBER 9; University of California: San Francisco, CA, 2006
5 Plotkin, S. S.; Onuchic, J. N. Quarterly Rev. Biophys. 2002, 35, 205
6 Shea, J.-E.; Brooks III, C. L. Annu. Rev. Phys. Chem. 2001, 52, 499   DOI   ScienceOn
7 Liwo, A.; Czaplewski, C.; Pillardy, J.; Scheraga, H. A. J. Chem. Phys. 2001, 115, 2323   DOI   ScienceOn
8 Yang, J. S.; Chen, W. W.; Skolnick, J.; Shakhnovich, E. I. Structure 2007, 15, 53   DOI   ScienceOn
9 Boas, F. E.; Harbury, P. B. Curr. Opin. Struct. Biol. 2007, 17, 199   DOI   ScienceOn
10 Quintilla, A.; Starikov, E.; Wenzel, W. J. Chem. Theory Comput. 2007, 3, 1183   DOI   ScienceOn
11 Verma, A.; Wenzel, W. BMC Struct. Biol. 2007, 7, 12   DOI   ScienceOn
12 Scheraga, H. A. Biopolymers 2007, 89, 479   DOI   ScienceOn
13 Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, Jr., K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179   DOI   ScienceOn
14 Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G. M.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J. M.; Kollman, P. J. Comput. Chem. 2003, 24, 1999
15 Dyson, H. J.; Sayre, J. R.; Meruka, G.; Shin, H.-C.; Lerner, R. A.; Wright, P. E. J. Mol. Biol. 1992, 226, 819   DOI
16 Plotkin, S. S.; Onuchic, J. N. Quarterly Rev. Biophys. 2002, 35, 111
17 Fiser, A.; Do, R. K. G.; Sali, A. Prot. Sci. 2000, 9, 1753   DOI   ScienceOn
18 Jones, D. T. J. Mol. Biol. 1999, 287, 797   DOI   ScienceOn
19 Floudas, C. A. Biotech. Bioeng. 2007, 97, 207   DOI   ScienceOn
20 Sali, A.; Blundell, T. L. J. Mol. Biol. 1993, 234, 779   DOI   ScienceOn
21 Wolynes, P. G. Phil. Trans. R. Soc. A 2005, 363, 453   DOI   ScienceOn
22 Petrey, D.; Honig, B. Mol. Cell 2005, 20, 811   DOI   ScienceOn
23 Summa, C. M.; Levitt, M.; Degrado, W. F. J. Mol. Biol. 2005, 352, 986   DOI   ScienceOn
24 Summa, C. M.; Levitt, M. Proc. Natl. Acad. Sci. USA 2007, 104, 3177   DOI   ScienceOn
25 Freidrichs, M. S.; Wolynes, P. G. Science 1989, 246, 371   DOI   ScienceOn
26 Hardin, C.; Eastwood, M. P.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 14235   DOI   ScienceOn
27 Hardin, C.; Eastwood, M. P.; Prentiss, M. C.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1679   DOI   ScienceOn
28 Zong, C.; Papoian, G. A.; Ulander, J.; Wolynes, P. G. J. Am. Chem. Soc. 2006, 128, 5168   DOI   ScienceOn
29 Prentiss, M. C.; Hardin, C.; Eastwood, M. P.; Zong, C.; Wolynes, P. G. J. Chem. Theory Comput. 2006, 2, 705   DOI   ScienceOn
30 Koretke, K. K.; Luthey-Schulten, Z.; Wolynes, P. G. Prot. Sci. 1996, 5, 1043
31 Andersen, C. A. F.; Palmer, A. G.; Brunak, S.; Rost, B. Structure 2002, 10, 175   DOI   ScienceOn
32 Onufriev, A.; Bashford, D.; Case, D. A. Proteins 2004, 55, 383   DOI   ScienceOn
33 Eastwood, M. P.; Hardin, C.; Luthey-Schulten, Z.; Wolynes, P. G. IBM J. Res. Dev. 2001, 45, 475   DOI
34 Aurora, R.; Creamer, T. P.; Srinivasan, R.; Rose, G. D. J. Biol. Chem. 1997, 272, 1413   DOI   ScienceOn
35 Cuff, J. A.; Clamp, M. E.; Siddiqui, A. S.; Finlay, M.; Barton, G. J. Bioinformatics 1998, 14, 892   DOI   ScienceOn
36 Mongan, J.; Simmerling, C.; McCammon, J. A.; Case, D. A.; Onufriev. A. J. Chem. Theory Comput. 2007, 3, 156   DOI   ScienceOn
37 Jimenez, M. A.; Munoz, V.; Rico, M.; Serrano, L. J. Mol. Biol. 1994, 242, 487
38 Saven, J. G.; Wolynes, P. G. J. Mol. Biol. 1996, 257, 199   DOI   ScienceOn
39 Myers, J. K.; Pace, C. N.; Scholtz, J. M. Proc. Natl. Acad. Sci. USA 1997, 94, 2833   DOI   ScienceOn
40 Dyson, H. J.; Merutka, G.; Waltho, J. P.; Lerner, R. A.; Wright, P. E. J. Mol. Biol. 1992, 226, 795   DOI
41 Jayachandran, G.; Vishal, V.; Garcia, A. E.; Pande, V. S. J. Struct. Biol. 2007, 157, 491   DOI   ScienceOn
42 Kim, D. E.; Yi, Q.; Gladwin, S. T.; Goldberg, J. M.; Baker, D. J. Mol. Biol. 1998, 284, 807   DOI   ScienceOn
43 Charkrabarty, A.; Baldwin, R. L. Adv. Protein Chem. 1995, 46, 141   DOI
44 Papoian, G. A.; Ulander, J.; Eastwood, M. P.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 3352   DOI   ScienceOn
45 Scott, K. A.; Alonso, D. O. V.; Sato, S.; Fersht, A. R.; Daggett, V. Proc. Natl. Acad. Sci. USA 2007, 104, 2661   DOI   ScienceOn
46 Sharpe, T.; Jonsson, A. L.; Rutherford, T. J.; Daggett, V.; Fersht, A. R. Prot. Sci. 2007, 16, 2233   DOI   ScienceOn
47 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   DOI   ScienceOn
48 Goldstein, R. A.; Luthey-Schulten, Z. A.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 4918, 9029
49 Rost, B.; Sander, C. J. Mol. Biol. 1993, 232, 584   DOI   ScienceOn
50 Krishna, M. M. G.; Maity, H.; Rumbley, J. N.; Lin, Y.; Englander, S. W. J. Mol. Biol. 2006, 359, 1410   DOI   ScienceOn
51 Ptitsyn, O. B. Dokl. Nauk. SSSR 1973, 210, 1213
52 Baldwin, R. L.; Rose, G. D. Trends Biochem. Sci. 1999, 24, 26   DOI   ScienceOn
53 Stryer, L. Biochemistry; W. H. Freeman and Company: New York, 1988
54 Bryngelson, J. D.; Hopfield, J. J.; Southard Jr., S. N. Tetrahedron Computer Methodology 1990, 3, 129   DOI
55 Oleververg, M.; Wolynes, P. G. Quarterly Rev. Biophys. 2005, 38, 405   DOI   ScienceOn
56 Munoz, V. Annu. Rev. Biophys. Biomol. Struct. 2007, 36, 395   DOI   ScienceOn
57 Zhang, Y.; Skolnick, J. Proc. Natl. Acad. Sci. USA 2005, 102, 1029   DOI   ScienceOn
58 Fersht, A. R. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding; W. H. Freeman and Co.: New York, 1999
59 Pollastri, G.; McLysaght, A. Bioinformatics 2005, 21, 1719   DOI   ScienceOn
60 Skolnick, J.; Kihara, D.; Zhang, Y. Proteins 2004, 56, 502   DOI   ScienceOn