Development of physics-based energy functions that predict medium-resolution structures for proteins of the α, β, and α/β structural classes

Journal of Physical Chemistry B

Volumn 105, Issue 30, 2001, Pages 7299-7311

  Pillardy, Jarosław ^a   Czaplewski, Cezary ^a,b   Liwo, Adam ^a,b   Wedemeyer, William J ^a   Lee, Jooyoung ^a,c   Ripoll, Daniel R ^a   Arłukowicz, Piotr ^a   Ołdziej, Stanisław ^a   Arnautova, Yelena A ^a   Scheraga, Harold A ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF GDA SK   (Poland)

^c Korea Institute for Advanced Study   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

VECTOR MONTE CARLO (VMC);

ENERGY GAP; FREE ENERGY; MONTE CARLO METHODS; POTENTIAL ENERGY; VECTORS;

PROTEINS;

EID: 0035797740     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0111012     Document Type: Article

References (42)

1. Liwo, A.; Pincus, M.R.; Wawak, R.J.; Rackovsky, S.; Scheraga, H.A. Protein Sci. 1993, 2, 1715.
2. Liwo, A.; Ołdziej, S.; Pincus, M.R.; Wawak, R.J.; Rackovsky, S.; Scheraga, H.A. J. Comput. Chem. 1997, 18, 849.
3. Liwo, A.; Pincus, M.R.; Wawak, R.J.; Rackovsky, S.; Ołdziej, S.; Scheraga, H.A. J. Comput. Chem. 1997, 18, 874.
4. Liwo, A.; Kaźmierkiewicz, R.; Czaplewski, C.; Groth, M.; Ołdziej, S.; Wawak, R.J.; Rackovsky, S.; Pincus, M.R.; Scheraga, H.A. J. Comput. Chem. 1998, 19, 259.
5. Liwo, A.; Pillardy, J.; Czaplewski, C.; Lee, J.; Ripoll, D.R.; Groth, M.; Rodziewicz-Motowidło, S.; Kaźmierkiewicz, R.; Wawak, R.J.; Ołdziej, S.; Scheraga, H.A., In RECOMB 2000, Proceedings of the Fourth Annual International Conference on Computational Molecular Biology; Shamir, R., Miyano, S., Istrail, S., Pevzner, P., Waterman, M., Eds.; ACM: New York, 2000, 193.
6. Liwo, A.; Pillardy, J.; Czaplewski, C.; Scheraga, H.A. J. Chem. Phys. in press.
7. Orengo, C.A.; Bray, J.E.; Hubbard, T.; LoConte, L.; Sillitoe, I. Proteins Struct. Funct. Genet. 1999, Suppl. 3, 149.
8. Sippl, M.J. J. Comput.-Aid. Mol. Des. 1993, 7, 473.
9. Skolnick, J.; Koliński, A.; Ortiz, A.R. J. Mol. Biol. 1997, 265, 217.
10. Bystroff, C.; Baker, D. J. Mol. Biol. 1998, 281, 565.
11. Liwo, A.; Lee, J.; Ripoll, D.R.; Pillardy, J.; Scheraga, H.A. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 5482.
12. Lee, J.; Liwo, A.; Ripoll, D.R.; Pillardy, J.; Scheraga, H.A. Proteins Struct. Funct. Genet. 1999, Suppl. 3, 204.
13. Anfinsen, C.B. Science 1973, 181, 223.
14. Honig, B.; Yang, A.-S. Adv. Protein Chem. 1995, 46, 27.
15. Momany, F.A.; McGuire, R.F.; Burgess, A.W.; Scheraga, H.A. J. Phys. Chem. 1975, 79, 2361.
16. Némethy, G.; Pottle, M.S.; Scheraga, H.A. J. Phys. Chem. 1983, 87, 1883.
17. Némethy, G.; Gibson, K.D.; Palmer, K.A.; Yoon, C.N.; Paterlini, G.; Zagari, A.; Rumsey, S.; Scheraga, H.A. J. Phys. Chem. 1992, 96, 6472.
18. Seetharamulu, P.; Crippen, G.M. J. Math. Chem. 1991, 6, 91.
19. Maiorov, V.N.; Crippen; G.M. J. Mol. Biol. 1992, 227, 876.
20. Mirny, L.A.; Shakhnovich; E.I. J. Mol. Biol. 1996, 264, 1164.
21. Hao, M.H.; Scheraga, H.A. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 4984.
22. Hao, M.H.; Scheraga, H.A. J. Phys. Chem., 1996, 100, 14540.
23. Dima, R.; Settanni, G.; Micheletti, C.; Banavar, J.R.; Maritan, A. J. Chem. Phys. 2000, 112, 9151.
24. Micheletti, C.; Seno, F.; Maritan, A.; Banavar, J.R. Comput. Mater. Sci. 2001, 20, 305.
25. Tobi, D.; Elber, R. Proteins Struct. Funct. Genet. 2000, 41, 40.
26. Lee, J.; Ripoll, D.R.; Czaplewski, C.; Pillardy, J.; Wedemeyer, W.J.; Scheraga, H.A. J. Phys. Chem. B 2001, 105, 7291.
27. Gay, J.G.; Berne, B.J. J. Chem. Phys. 1981, 74, 3316.
28. Bernstein, F.C.; Koetzle, T.F.; Williams, G.J.B.; Meyer, E.F., Jr.; Brice, M.D.; Rodgers, J.R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. J. Mol. Biol. 1977, 112, 535.
29. Lee, J.; Scheraga, H.A.; Rackovsky, S. J. Comput. Chem. 1997, 18, 1222.
30. Lee, J.; Scheraga, H.A.; Rackovsky, S. Biopolymers 1998, 46, 103.
31. Lee, J.; Scheraga, H.A. Int. J. Quantum Chem. 1999, 75, 255.
32. Assa-Munt, N.; Mortishire-Smith, R.J.; Aurora, R.; Herr, W.; Wright, P.E. Cell 1993, 73, 193.
33. Downing, A.K.; Driscoll, P.C.; Harvey, T.S.; Dudgeon, T.J.; Smith, B.O.; Baron, M.; Campbell, I.D. J. Mol. Biol. 1992, 225, 821.
34. Gouda, H.; Torigoe, H.; Saito, A.; Sato, M.; Arata, Y.; Shimada, I. Biochemistry 1992, 31, 9665.
35. Kortemme, T.; Ramirez-Alvarado, M.; Serrano, L. Science 1998, 281, 253.
36. Skelton, N.J.; Kordel, J.; Chazin, W.J. J. Mol. Biol. 1995, 249, 441.
37. Dahiyat, B.I.; Mayo, S.L. Science 1997, 278, 82.
38. Pillardy, J.; Czaplewski, C.; Liwo, A.; Lee, J.; Ripoll, D.R.; Kazmierkiewicz, R.; Oldziej, S.; Wedemeyer, W.J.; Gibson, K.D.; Arnautova, Y.A.; Saunders J.; Ye, Y.-J.; Scheraga, H.A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 2329.
39. Dill, K.A.; Bromberg, S.; Yue, K.; Fiebig, K.M.; Yee, D.P.; Thomas, P.D.; Chan, H.S. Protein Sci. 1995, 4, 561.
40. Lau, K.F.; Dill, K.A. Macromolecules 1989, 22, 3986.
41. Miyazawa, S.; Jernigan, R.L. Macromolecules 1985, 18, 534.
42. Kondrak, G.; van Beek, P. Artificial Intelligence 1997, 89, 365.