DOMPLOT: A program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts

Protein Engineering

Volumn 12, Issue 5, 1999, Pages 375-379

  Todd, A E ^a   Orengo, C A ^a   Thornton, J M ^a,b  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Protein domains; Protein structure; Protein ligand contacts; Schematic diagrams; Sequence motifs

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; LIGAND BINDING; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

EID: 0033033274     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/12.5.375     Document Type: Article

References (30)

1. Adobe Systems Inc. (1985) Postscript Language Reference Manual. Addison Wesley Press, Reading, MA.
2. Bairoch, A., Bucher, P. and Hofmann, K. (1997) Nucleic Acid. Res., 25, 217-221.
3. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) J. Mol. Biol., 112, 535-542.
4. Branden, C.-I. (1991) Curr. Opin. Struct. Biol., 1, 978-983.
5. Farber, G.K. and Petsko, G.A. (1990) Trends Biochem. Sci., 15, 228-234.
6. Fox, K. and Karplus, P.A. (1994) Structure, 2, 1089-1105.
7. Gouzy, J., Eugene, P. Greene, E.A., Kahn, D. and Corpet, F. (1997) Comput. Appl. Biosci., 13, 601-608.
8. Holm, L. and Sander, C. (1994) Proteins, 19, 256-268.
9. Islam, S.A., Luo, J. and Sternberg, M.J.E. (1995) Protein Engng, 8, 513-525.
10. Jones, S., Stewart, M., Michie, A., Swindells, M.B., Orengo, C. and Thornton, J.M. (1998) Protein Sci., 7, 233-242.
11. Kabsch, W. and Sander, C. (1983) Biopolymers, 22, 2577-2637.
12. Karplus, P.A., Fox, K.M. and Massey, V. (1995) FASEB J., 9, 1518-1526.
13. Kasuya, A. and Thornton, J.M. (1999) J. Mol. Biol., 286, 1673-1691.
14. Kraulis, P.J. (1991) J. Appl. Crystallogr., 24, 946-950.
15. Lim, L.W., Shamala, N., Mathews, F.S., Steenkamp, D.J., Hamlin, R. and Xuong, N. (1986) J. Biol. Chem., 261, 15140-15146.
16. Lindqvist, Y. (1989) J. Mol. Biol., 209, 151-166.
17. Lindqvist, Y., Branden, C.-I., Mathews, F.S. and Lederer, F. (1991) J. Biol. Chem., 266, 3198-3207.
18. McDonald, I.K. and Thornton, J.M. (1994) J. Mol. Biol., 238, 777-793.
19. Milbum, D., Laskowski, R. and Thornton, J.M. (1998) Protein Engng, 11, 855-859.
20. O'Brien, M.C. and McKay, D.B. (1993) J. Biol. Chem., 268, 19656-19658.
21. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B. and Thornton, J.M. (1997) Structure, 5, 1093-1108.
22. Orengo, C.A. (1998) Protein Sci., in press.
23. Richardson, J.S. (1981) Adv. Protein Chem., 34, 246-253.
24. Schultz, J., Milpetz, F., Bork, P. and Ponting, C.P. (1998) Proc. Natl Acad. Sci. USA, 95, 5857-5864.
25. Scrutton, N.S. (1994) BioEssays, 16, 115-122.
26. Siddiqui, A.S. and Barton, G.J. (1995) Protein Sci., 4, 872-884.
27. Swindells, M.B. (1995) Protein Sci., 4, 103-112.
28. Taylor, W.R. and Orengo, C.A. (1989) J. Mol. Biol., 208, 1-22.
29. Wilmanns, M., Hyde, C.C., Davies, D.R., Kirschner, K. and Jansonius, J.N. (1991) Biochemistry, 30, 9161-9169.
30. Xia, Z.-X. and Mathews, F.S. (1990) J. Mol. Biol., 212, 837-863.