Multiple structural alignment for distantly related all β structures using TOPS pattern discovery and simulated annealing

Protein Engineering

Volumn 16, Issue 12, 2003, Pages 913-923

  Williams, A ^a   Gilbert, D R ^b   Westhead, D R ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

Pattern discovery; Protein topology; Simulated annealing; Structural alignment; Superfolds

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BETA SHEET; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SIMULATION; STRUCTURE ANALYSIS; TECHNIQUE;

PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 1442286046     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (42)

1. Alexandrov, N.N. and Go, N. (1994) Protein Sci., 3, 866-875.
2. Argos, P. and Rossmann, M. (1976) J. Mol. Biol., 105, 75-95.
3. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) Nucleic Acids Res., 28, 235-242.
4. Brändon, C.I. and Tooze, J. (1991) In Brändon, C.I. and Tooze, J. (eds), Introduction to Protein Structure. Garland Publishing, New York, pp. 43-57.
5. Brazma, A., Jonassen, I., Eidhammer I. and Gilbert D.R. (1998) J. Comput. Biol., 5, 277-303.
6. Flores, T.P.J., Moss, D.M. and Thornton, J.M. (1994) Protein Eng., 7, 31-37.
7. Gerlt, J.A. (2000) Nat. Struct. Biol., 7, 171-173.
8. Gilbert, D.R., Westhead, D.R., Nagano, N. and Thornton, J.M. (1999) Bioinformatics, 15, 317-326.
9. Gilbert, D.R., Westhead, D.R., Viksna, J. and Thornton, J.M. (2001) J. Comput. Chem., 26, 23-30.
10. Grindley, H.M., Artymiuk, P.J., Rice, D.W. and Willet, P. (1993) J. Mol. Biol., 229, 707-721.
11. Guda, C., Scheef, E.D., Bourne, P.E. and Shindyalov, I.N. (2001) Pac. Symp. Biocomput., 6, 275-286.
12. Harrison, A., Pearl, F., Mott, R., Thornton, J. and Orengo, C. (2002) J. Mol. Biol., 323, 909-926.
13. Hirosawa, M., Hoshida, M., Ishikawa, M. and Toya, T. (1993) Comput. Appl. Biosci., 9, 161-167.
14. Holm, L. and Sander, C. (1993) J. Mol. Biol., 233, 123-138 (see also: http://www.ebi.ac.uk/dali/domain).
15. Holm, L. and Sander, C. (1996) Science, 273, 595-602.
16. Ishikawa, M., Toya, T., Hoshida, M., Nitta, K., Ogiwara, A. and Kanehisa, M. (1993) Comput. Appl. Biosci., 9, 267-273.
17. Kabsch, W. (1976) Acta Crystallogr. A, 32, 922-923.
18. Kim, J., Paramanik, S. and Chung, M.J. (1994) Comput. Appl. Biosci., 10, 419-426.
19. Kirkpatrick, S., Gerlatt, C.D. and Vecchi, M.P. (1983) Science, 220, 671-680.
20. Koch, I., Lengauer, T. and Wanke, E. (1996) J. Comput. Biol., 3, 289-306.
21. Lackner, P., Koppensteiner, W.A., Sippl, M.J. and Domingues, F.S. (2000) Protein Eng., 13, 745-752.
22. McLachlan, A.D. (1972) Acta Crystallogr. A, 28, 656-657.
23. Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H. and Teller, E. (1953) J. Chem. Phys., 21, 1087-1092.
24. Murzin, A. (1993) EMBO J., 12, 861-867.
25. Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) J. Mol. Biol., 247, 536-540 (see also: http://scop.mrc-lmb.cam.ac.uk/scop).
26. Nagano, N., Orengo, C.A. and Thornton, J.M. (2002) J. Mol. Biol., 321, 741-765.
27. Needleman, S.B. and Wunsch, C.D. (1970) J. Mol. Biol., 48, 443-453.
28. Notredame, C. and Higgins, D.G. (1996) Nucleic Acids Res., 24, 1515-1524.
29. Orengo, C.A. and Taylor, W.R. (1990) J. Theor. Biol., 147, 517-551.
30. Orengo, C.A., Jones, D.T. and Thornton, J.M. (1994) Nature, 372, 631-634.
31. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B. and Thornton, J.M. (1997) Structure, 5, 1093-1108 (see also: http://www.biochem.ucl.ac.uk/bsm/cath).
32. Pajados, G. and Palau, J. (1999) Biologia, 54, 231-254.
33. Richardson, J.S. (1981) Adv. Protein Chem., 34, 167-339.
34. Russell, R.B. and Barton, G.J. (1992) Proteins Struct. Funct. Genet., 14, 309-323.
35. Sali, A. and Blundell, T.L. (1990) J. Mol. Biol., 212, 403-428.
36. Shindyalov, I.N and Bourne, P.E. (1998) Protein Eng., 11, 739-747.
37. Sutcliffe, M.J., Haneef, I., Carney, D. and Blundell, T.L. (1987) Protein Eng., 1, 377-384.
38. Szustakowski, J.D. and Weng, Z. (2000) Proteins Struct. Funct. Genet., 38, 428-440.
39. Taylor, W.R. and Orengo, C.A. (1989a) Protein Eng., 2, 505-519.
40. Taylor, W.R. and Orengo, C.A. (1989b) J. Mol. Biol., 208, 1-21.
41. Viksna, J. and Gilbert, D.R. (2001) WABI2001: 1st Workshop on Algorithms in Biolnformatics, LNCS 2149, pp. 98-111.
42. Westhead, D.R., Hatton, D.C. and Thornton, J.M. (1998) Trends Biochem. Sci., 23, 35-36 (see also: http://www3.ebi.ac.uk/tops).