Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field

Protein Engineering, Design and Selection

Volumn 21, Issue 12, 2008, Pages 729-735

  Cui, Meng ^a,b   Mezei, Mihaly ^a   Osman, Roman ^a  

^a NEW YORK UNIVERSITY   (United States)

^b VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

Implicit solvent; Local move Monte Carlo; Potential map; Protein loop prediction; Simulated annealing

Indexed keywords

ANNEALING; CRYSTAL STRUCTURE; FORECASTING; GLOBAL OPTIMIZATION; MONTE CARLO METHODS; QUALITY CONTROL; STATISTICAL TESTS;

COMPUTATIONAL COSTS; ENERGY EVALUATIONS; ENERGY LOOPS; FORCE FIELDS; GRID-BASED; HOMOLOGY MODELS; IMPLICIT SOLVENT; LOCAL MOVE MONTE CARLO; LOCAL MOVES; LOOP CONFORMATIONS; LOOP REGIONS; MONTE CARLO; MONTE CARLO APPROACHES; POTENTIAL MAP; PREDICTION METHODS; PREDICTION QUALITIES; PROTEIN DOCKING; PROTEIN LOOP PREDICTION; PROTEIN LOOPS; ROOT MEAN SQUARES; SIDE CHAINS; SOLVATION EFFECTS; TEST CASES; TORSION ANGLES;

SIMULATED ANNEALING;

ARTICLE; CRYSTAL STRUCTURE; HYDROGEN BOND; MONTE CARLO METHOD; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SAMPLING; SOLVATION;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; HYDROPHOBICITY; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEINS; SENSITIVITY AND SPECIFICITY; SOLUBILITY; STATIC ELECTRICITY;

EID: 56549099908     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzn056     Document Type: Article

References (63)

1. Bajorath,J. and Sheriff,S. (1996) Proteins, 24, 152-157.
2. Brooks,B.R., Bruccoleri,R.E., Olafson,B.D., States,D.J., Swaminathan,S. and Karplus,M. (1983) J. Comp. Chem., 4, 187-217.
3. Brower,R.C., Vasmatzis,G., Silverman,M. and Delisi,C. (1993) Biopolymers, 33, 329-334.
4. Bruccoleri,R.E. and Karplus,M. (1985) Macromolecules, 18, 1767-1773.
5. Bruccoleri,R.E. and Karplus,M. (1987) Biopolymers, 26, 137-168.
6. Carlacci,L. and Englander,S.W. (1993) Biopolymers, 33, 1271-1286.
7. Chothia,C. and Lesk,A.M. (1987) J. Mol. Biol., 196, 901-917.
8. Collura,V., Higo,J. and Garnier,J. (1993) Protein Sci., 2, 1502-1510.
9. Cornell,W.D., Cieplak,P., Bayly,C.I., Gould,I.R., Merz,K.M., Ferguson,D., Spellmeyer,D.C., Fox,T., Caldwell,J.W. and Kollman,P.A. (1995) J. Am. Chem. Soc., 117, 5179-5197.
10. Das,B. and Meirovitch,H. (2001) Proteins, 43, 303-314.
11. de Bakker,P.I., DePristo,M.A., Burke,D.F. and Blundell,T.L. (2003) Proteins, 51, 21-40.
12. Deane,C.M. and Blundell,T.L. (2000) Proteins, 40, 135-144.
13. Deane,C.M. and Blundell,T.L. (2001) Protein Sci., 10, 599-612.
14. Deem,M.W. and Bader,J.S. (1996) Mol. Phys., 87, 1245-1260.
15. Dinner,A.R. (2000) J. Comp. Chem., 21, 1132.
16. Dodd,L.R., Boone,T.D. and Theodorou,D.N. (1993) Mol. Phys., 78, 961-996.
17. Fernandez-Fuentes,N., Oliva,B. and Fiser,A. (2006) Nucleic Acids Res., 34, 2085-2097.
18. Fetrow,J.S., Dreher,U., Wiland,D.J., Schaak,D.L. and Boose,T.L. (1998) Protein Sci., 7, 994-1005.
19. Fine,R.M., Wang,H., Shenkin,P.S., Yarmush,D.L. and Levinthal,C. (1986) Proteins, 1, 342-362.
20. Fiser,A. and Sali,A. (2003) Bioinformatics, 19, 2500-2501.
21. Fiser,A., Do,R.K. and Sali,A. (2000) Protein Sci., 9, 1753-1773.
22. Go,N. and Scheraga,H.A. (1970) Macromolecules, 3, 178-187.
23. Greer,J. (1980) Proc. Natl Acad. Sci. USA, 77, 3393-3397.
24. Guex,N. and Peitsch,M.C. (1997) Electrophoresis, 18, 2714-2723.
25. Higo,J., Collura,V. and Garnier,J. (1992) Biopolymers, 32, 33-43.
26. Hoffmann,D. and Knapp,W. (1996) Eur. Biophys. J., 24, 387.
27. Huey,R., Morris,G.M., Olson,A.J. and Goodsell,D.S. (2007) J. Comp.Chem., 28, 1145-1152.
28. Im,W., Lee,M.S. and Brooks,C.L., III (2003) J. Comp. Chem., 24, 1691-1702.
29. Jacobson,M.P., Pincus,D.L., Rapp,C.S., Day,T.J., Honig,B., Shaw,D.E. and Friesner,R.A. (2004) Proteins, 55, 351-367.
30. Jones,T.A. and Thirup,S. (1986) EMBO J., 5, 819-822.
31. Joseph,D., Petsko,G.A. and Karplus,M. (1990) Science, 249, 1425-1428.
32. Liu,P., Huang,C., Wang,H.L., Zhou,K., Xiao,F.X. and Qun,W. (2004) FEBS Lett., 577, 205-208.
33. MacKerell,A.D., Jr. et al. (1998) J. Phys. Chem. B, 102, 3586-3616.
34. McGarrah,D.B. and Judson,R.S. (1993) J. Comp. Chem., 14, 1385.
35. Mehler,E.L. and Solmajer,T. (1991) Protein Eng., 4, 903-910.
36. Mehler,E.L., Hassan,S.A., Kortagere,S. and Weinstein,H. (2006) Proteins, 64, 673-690.
37. Mezei,M. (2003) J. Chem. Phys., 118, 3874-3879.
38. Michalsky,E., Goede,A. and Preissner,R. (2003) Protein Eng., 16, 979-985.
39. Morris,G.M., Goodsell,D.S., Halliday,R.S., Huey,R., Hart,W.E., Belew,R.K. and Olson,A.J. (1998) J. Comp. Chem., 19, 1639-1662.
40. Moult,J. and James,M.N. (1986) Proteins, 1, 146-163.
41. Peng,H.P. and Yang,A.S. (2007) Bioinformatics, 23, 2836-2842.
42. Ragona,L., Fogolari,F., Catalano,M., Ugolini,R., Zetta,L. and Molinari,H. (2003) J. Biol. Chem., 278, 38840-38846.
43. Rapp,C.S. and Friesner,R.A. (1999) Proteins, 35, 173-183.
44. Ring,C.S. and Cohen,F.E. (1994) Isr. J. Chem., 34, 245-252.
45. Rohl,C.A., Strauss,C.E., Chivian,D. and Baker,D. (2004) Proteins, 55, 656-677.
46. Rosenbach,D. and Rosenfeld,R. (1995) Protein Sci., 4, 496-505.
47. Samudrala,R. and Moult,J. (1998) J. Mol. Biol., 275, 895-916.
48. Shenkin,P.S., Yarmush,D.L., Fine,R.M., Wang,H.J. and Levinthal,C. (1987) Biopolymers, 26, 2053-2085.
49. Sippl,M.J. (1990) J. Mol. Biol., 213, 859-883.
50. Smith,K.C. and Honig,B. (1994) Proteins, 18, 119-132.
51. Soto,C.S., Fasnacht,M., Zhu,J., Forrest,L. and Honig,B. (2008) Proteins, 70, 834-843.
52. Spassov,V.Z., Flook,P.K. and Yan,L. (2008) Protein Eng. Des. Sel., 21, 91-100.
53. van Vlijmen,H.W. and Karplus,M. (1997) J Mol Biol, 267, 975-1001.
54. Wedemeyer,W.J. and Scheraga,H.A. (1999) J. Comp. Chem., 20, 819-844.
55. Wesson,L. and Eisenberg,D. (1992) Protein Sci., 1, 227-235.
56. Wlodawer,A., Miller,M., Jaskolski,M., Sathyanarayana,B.K., Baldwin,E., Weber,I.T., Selk,L.M., Clawson,L., Schneider,J. and Kent,S.B. (1989) Science, 245, 616-621.
57. Wu,M.G. and Deem,M.W. (1999a) J. Chem. Phys., 111, 6625.
58. Wu,M.G. and Deem,M.W. (1999b) Mol. Phys., 97, 559-580.
59. Xiang,Z., Soto,C.S. and Honig,B. (2002) Proc. Natl Acad. Sci. USA, 99, 7432-7437.
60. Zheng,Q. and Kyle,D.J. (1996) Proteins, 24, 209-217.
61. Zheng,Q., Rosenfeld,R., Vajda,S. and DeLisi,C. (1993) Protein Sci., 2, 1242-1248.
62. Zhang,H., Lai,L., Wang,L., Han,Y. and Tang,Y. (1997) Biopolymers, 41, 61-72.
63. Zhu,K., Pincus,D.L., Zhao,S. and Friesner,R.A. (2006) Proteins, 65, 438-452.