Peptide backbone reconstruction using dead-end elimination and a knowledge-based forcefield

Journal of Computational Chemistry

Volumn 25, Issue 1, 2004, Pages 16-27

  Adcock, Stewart A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Dead end elimination; Knowledge based forcefield; Protein backbone

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; CONFORMATIONS; CRYSTAL ATOMIC STRUCTURE; CRYSTAL STRUCTURE; MOLECULAR STRUCTURE;

DEAD END ELIMINATION; KNOWLEDGE BASED FORCEFIELD; PEPTIDE BACKBONE RECONSTRUCTION; PUTATIVE CONFORMATIONS;

POLYPEPTIDES;

PEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; HYDROGEN BOND; PROTEIN CONFORMATION; SYNTHESIS; THEORETICAL MODEL; THERMODYNAMICS;

HYDROGEN BONDING; MODELS, MOLECULAR; MODELS, THEORETICAL; PEPTIDES; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 0346394782     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.10314     Document Type: Article

References (47)

1. Jones, T.; Thirup, S. EMBO J 1986, 5, 819.
2. Reid, L.; Thornton, J. Proteins Struct Funct Genet 1989, 5, 170.
3. Claessens, M.; van Cutsem, E.; Lasters, I.; Wodak, S. Protein Eng 1989, 2, 335.
4. Holm, L.; Sander, C. J Mol Biol 1991, 218, 183.
5. Levitt, M. J Mol Biol 1992, 226, 507.
6. Payne, P. Protein Sci 1993, 2, 315.
7. Rey, A.; Skolnick, J. J Comput Chem 1992, 13, 443.
8. Bassolino-Klimas, D.; Buccoleri, R. Proteins Struct Funct Genet 1992, 14, 465.
9. Milik, M.; Kolinski, A.; Skolnick, J. J Comput Chem 1997, 18, 80.
10. Feldman, H.; Hogue, C. Proteins Struct Funct Genet 2000, 39, 112.
11. Liwo, A.; Pincus, M.; Wawak, R.; Rackovsky, S.; Scheraga, H. Protein Sci 1993, 2, 1697.
12. Iwata, Y.; Kasuya, A.; Miyamoto, S. J Mol Graph Model 2002, 21, 119
13. Correa, P. Protein Struct Funct Genet 1990, 7, 366.
14. van Gelder, C.; Leusen, F.; Leunissen, J.; Noordik, J. Proteins Struct Funct Genet 1994, 18, 174.
15. van Hooft, P.; Holtje, H.-D. J Computer-Aided Mol Des 2000, 14, 719.
16. Mathiowetz, A.; Goddard, W., III Protein Sci 1995, 4, 1217.
17. Gan, K.; Coxon, J.; McKinnon, A.; Worth, G. Biopolymers 1997, 41, 391.
18. Kazmierkiewicz, R.; Liwo, A.; Scheraga, H. J Comput Chem 2002, 23, 715.
19. Lee, M.; Duan, Y.; Kollman, P. Proteins Struct Funct Genet 2000, 39, 309.
20. Miyazawa, S.; Jernigan, R. L. Macromolecules 1985, 18, 534.
21. Sippl, M. J Mol Biol 1990, 213, 849.
22. Rooman, M. J.; Kocher, J. P.; Wodak, S. J. J Mol Biol 1991, 221, 961.
23. Jones, D. T.; Taylor, W. R.; Thornton, J. Nature 1992, 358, 86.
24. Kocher, J. A.; Rooman, M. J.; Wodak, S. J. J Mol Biol 1994, 235, 158.
25. Bahar, I.; Jernigan, R. L. J Mol Biol 1997, 266, 195.
26. Wodak, S. J. In Encyclopedia of Computational Chemistry; Schleyer, P. R., Ed.; John Wiley & Sons: New York, 1998.
27. Thomas, P.; Dill, K. J Mol Biol 1996, 257, 457.
28. Jernigan, R. L.; Bahar, I. Curr Opin Struct Biol 1996, 6, 195.
29. Berman, H.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.; Weissig, H.; Shindyalov, I.; Bourne, P. Nucleic Acids Res 2000, 28, 235.
30. Altenbach, C.; Madden, T. L.; Schaffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J. Nucleic Acids Res 1997, 25, 3389.
31. http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi, "NCBI Tool-Box," 2003.
32. McDonald, I.; Thornton, J. J Mol Biol 1994, 238, 777.
33. Desmet, J.; De Maeyer, M.; Hazes, B.; Lasters, I. Nature 1992, 356, 539.
34. Goldstein, R. Biophys J 1994, 66, 1335.
35. Looger, L.; Hellinga, H. J Mol Biol 2001, 307, 429.
36. Lasters, I.; Desmet, J. Protein Eng 1993, 6, 717.
37. Desmet, J.; De Maeyer, M.; Lasters, I. In The Protein Folding Problem and Tertiary Structure Prediction; Merz, K. M., Jr.; Le Grand, S. M., Eds.; Birkhauser: Boston, 1994.
38. Gordon, D.; Mayo, S. J Comput Chem 1998, 19, 1505.
39. Kearsley, S. K. Acta Crystallogr Sect A 1989, 45, 208.
40. Park, B.; Levitt, M. J Mol Biol 1996, 258, 367.
41. Samudrala, R.; Xia, Y.; Huang, E.; Levitt, M. Proteins Struct Funct Genet 1999, Suppl. 3, 194.
42. Simons, K.; Kooperberg, C.; Huang, E.; Baker, D. J Mol Biol 1997, 268, 209.
43. http://www.ebi.ac.uk/maxsprout/, "MaxSprout: Reconstruction of 3D coordinates from C(alpha) trace," 2002.
44. Leach, A. R.; Lemon, A. Proteins 1998, 33, 227.
45. Lemak, A.; Gunn, J. J Phys Chem B 2000, 104, 1097.
46. Samudrala, R.; Moult, J. J Mol Biol 1998, 275, 893.
47. Fain, B.; Xia, Y.; Levitt, M. Protein Sci 2002, 11, 2010.