Protein loops on structurally similar scaffolds: Database and conformational analysis

Biopolymers

Volumn 49, Issue 6, 1999, Pages 481-495

  Li, Weizhong ^a   Liu, Zhijie ^a   Lai, Luhua ^a  

^a Peking University   (China)

Author keywords

Data base; Loop conformation; Loop modeling; Loop structure; Protein loop

Indexed keywords

CONFORMATIONS; DATABASE SYSTEMS; INTERNET; MOLECULAR STRUCTURE; ONLINE SEARCHING;

AVERAGE LINKAGE CLUSTER ANALYSIS METHOD; LOOP CONFORMATION;

PROTEINS;

AMINO ACID SEQUENCE; ARTICLE; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; DATABASES, FACTUAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE ALIGNMENT;

EID: 0033134684     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0282(199905)49:6<481::AID-BIP6>3.0.CO;2-V     Document Type: Article

References (45)

1. Venkatachalam, C. M. Biopolymers 1968, 6, 1425-1436.
2. Richardson, J. S. Adv Protein Chem 1981, 34, 167-339.
3. Sibanda, B. L.; Thornton, J. M. Nature 1985, 316, 170-174.
4. Milner, W. E.; Poet, R. Biochem J 1986, 240, 289-292.
5. Milner-White, E. J.; Poet, R. Trends Biochem Sci 1987, 12, 189-192.
6. Sibanda, B. L.; Blundell, T. L.; Thornton, J. M. J Mol Biol 1989, 206, 759-777.
7. Efimov, A. V. Protein Eng 1991, 4, 245-250.
8. Wintjens, R. T.; Rooman, M. J.; Wodak, S. J. J Mol Biol 1996, 255, 235-253.
9. Leszczynski, J. F.; Rose, G. D. Science 1986, 234, 849-855.
10. Ring, C. S.; Kneller, D. G.; Langridge, R.; Cohen, F. E. J Mol Biol 1992, 224, 685-699.
11. Martin, A. C. R.; Toda, K.; Stirk, H. J.; Thornton, J. M. Protein Eng 1995, 8, 1093-1101.
12. Chothia, C.; Lesk, A. M.; Levitt, M.; Amit, A. G.; Mariuzza, R. A.; Phillips, S. E. V.; Poljak, R. J. Science 1986, 233, 755-758.
13. Chothia, C.; Lesk, A. M. J Mol Biol 1987, 196, 901-917.
14. Chothia, C.; Lesk, A. M.; Tramontano, A.; Levitt, M.; Smith-Gill, S. J.; Air, G.; Sheriff, S.; Padlan, E. A.; Davies, D.; Tulip, W. R.; Colman, P. M.; Spinelli, S.; Alzari, P. M.; Poljak, R. J. Nature 1989, 342, 877-883.
15. Chothia, C.; Lesk, A. M.; Gherardi, E.; Tomlinson, I. M.; Walter, G.; Marks, J. D.; Llewelyn, M. B.; Winter. G. J Mol Biol 1992, 227, 799-817.
16. Martin, A. C. R.; Cheetham, J. C.; Rees, A. R. Proc Natl Acad Sci USA 1989, 86, 9268-9272.
17. Martin, A. C. R.; Thornton, J. M. J Mol Biol 1996, 263, 800-815.
18. 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, 535-542.
19. Mosimann, S.; Meleshko, R.; James, M. N. G. Proteins Struct Funct Genet 1995, 23, 301-317.
20. Šali, A. Curr Opin Struct Biol 1995, 6, 437-451.
21. Ei Hawrani, A. S.; Moreton, K. M.; Sessions, R. B.; Clarke, A. R.; Holbrook, J. J. TIBTECH 1994, 12, 207-211.
22. Jones, T. A.; Thirup, T. EMBO J 1986, 5, 819-822.
23. Blundell, T.; Carney, D.; Gardner, S.; Hayes, F.; Howlin, B.; Hubbard, T.; Overington, J.; Sigh, O. A.; Sibanda, B. L.; Sutcliffe, M. Eur J Biochem 1988, 172, 513-520.
24. Topham, C.; McLeod, A.; Eisenmenger, F.; Overington, J. P.; Johnson, M. S.; Blundell, T. L. J Mol Biol 1993, 229, 194-220.
25. Rufino, S. D.; Donate, L. E.; Canard, L. H. J.; Blundell, T. L. J Mol Biol 1997, 267, 352-367.
26. Sudarsanam, S.; DuBose, R. F.; March, C. J.; Srinivasan, S. Protein Sci 1995, 4, 1412-1420.
27. Collura, V.; Higo, J.; Garnier, J. Protein Sci 1993, 2, 1502-1510.
28. Higo, J.; Collura, V.; Garnier, J. Biopolymers 1992, 32, 33-43.
29. Mas, M. T.; Smith, K. C.; Yarmush, D. L.; Aisaka, K.; Fine, R. M. Proteins Struct Funct Genet 1992, 14, 483-498.
30. Zhang, H.; Lai, L.; Wang, L.; Han, Y.; Tang, Q. Biopolymers 1997, 41, 61-72.
31. Zheng, Q.; Rosenfeld, R.; DeLisi, C.; Kyle, D. J. Protein Sci 1994, 3, 493-506.
32. Zheng, Q.; Kyle, D. J. Proteins Struct Funct Genet 1994, 19, 324-329.
33. Zheng, Q.; Kyle, D. J. Proteins Struct Funct Genet 1996, 24, 209-217.
34. Kwasigroch, J.; Chomilier, J.; Mornon, J. J Mol Biol 1996, 259, 855-872.
35. Donate, L. E.; Rufino, S. D.; Canard, L. H. J.; Blundell, T. L. Protein Sci 1996, 5, 2600-2616.
36. Oliva, B.; Bates, P. A.; Querol, E.; Avilés, F. X.; Sternberg, M. J. E. J Mol Biol 1997, 266, 814-830.
37. van Vlijmen, H. W. T.; Karplus, M. J Mol Biol 1997, 267, 975-1001.
38. Holm, L.; Ouzounis, C.; Sander, C.; Tuparev, G.; Vriend, G. Protein Sci 1992, 1, 1691-1698.
39. Holm, L.; Sander, C. J Mol Biol 1993, 233, 123-138.
40. Holm, L.; Sander, C. Nucleic Acids Res 1994, 22, 3600-3609.
41. Holm, L.; Sander, C. Nucleic Acids Res 1997, 25, 231-234.
42. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577-2637.
43. Pearson, W. R.; Lipman, D. J. Proc Natl Acad Sci USA 1988, 85, 2444-2448.
44. Murzin, A. G.; Brenner, S. E.; Hubbard, T.; Chothia, C. J Mol Biol 1995, 247, 536-540.
45. Topham, C. M.; McLeod, A.; Eisenmenger, F.; Overington, J. P.; Johnson, M. S.; Blundell, T. L. J Mol Biol 1993, 229, 194-220.