| 1. |
Orengo, C. A., Swindells, M. B., Michie, A. D., Zvelebil, M. J., Driscoll, P. C., Waterfield, M. D., and Thornton, J. M. (1995)
Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural
similarity. Protein Sci.
4, 1977–1983.
|
| |
| 2. |
Colloc’h, N., Etchebest, C., Thoreau, E., Henrissat, B., and Mornon, J. P. (1993) Comparison of three algorithms for the assignment
of secondary structure in proteins: the advantages of a consensus assignment. Protein Eng.
6, 377–382
|
| |
| 3. |
Frishman, D. and Argos, P. (1995) Knowledge-based protein secondary structure assignment. Proteins: Struct. Funct. Genet.
23, 566–579.
|
| |
| 4. |
Taylor, W. R. (1992) Patterns, predictions and problems, in Patterns in Protein Sequence and Structure (Taylor, W. R., ed.), Springer-Verlag, Berlin.
|
| |
| 5. |
Sternberg, M. J. E., Hegyi, H., Islam, S. A., Luo, J., and Russell, R. B. (1995) Towards an intelligent system for the automatic
assignment of domains in globular proteins. Ismb
3, 376–383.
|
| |
| 6. |
McLachlan, A. D. (1979) Gene duplications in the structural evolution of chymotrypsin. J. Mol. Biol.
128, 49–79.
|
| |
| 7. |
Holm, L. and Sander, C. (1994) Parser for protein folding units. Proteins: Struct. Funct. Genet.
19, 256–268.
|
| |
| 8. |
Siddiqui, A. S. and Barton, G. J. (1995) Continuous and discontinuous domains: an algorithm for the automatic generation of
reliable protein domain definitions. Protein Sci.
94, 872–884.
|
| |
| 9. |
Sowdhamini, R. and Blundell, T. L. (1995) An automated method involving cluster analysis of secondary structures for the identification
of domains in proteins. Protein Sci.
4, 506–520.
|
| |
| 10. |
Islam, S. A., Luo, J., and Sternberg, M. J. E. (1995) Identification and analysis of domains in proteins. Protein Eng.
8, 513–525.
|
| |
| 11. |
Swindells, M. B. (1995) A procedure for detecting structural domains in proteins, Protein Sci.
4, 103–112
|
| |
| 12. |
Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B., and Thornton, J. M. (1997) CATH—a hierarchic classification
of protein domain structures. Structure
5, 1093–1108.
|
| |
| 13. |
Jones S., Stewart M., Michie A., Swindells M. B., Orengo C., and Thornton, J. M. (1998) Domain assignment for protein structures
using a consensus approach: characterization and analysis. Protein Sci.
7, 233–242.
|
| |
| 14. |
Holm, L. and Sander, C. (1998) Dictionary of recurrent domains in protein structures. Proteins: Struct. Funct. Genet.
33, ???-???.
|
| |
| 15. |
Russell, R. B. (1994) Domain insertion. Protein Eng.
7, 1407–1410.
|
| |
| 16. |
Levitt, M. and Chothia, C. (1976) Structural patterns in globular proteins. Nature
261, 552–558.
|
| |
| 17. |
Murzin, A. G., Brenner, S. E., Hubbard, T. J., and Chothia, C. (1995) SCOP: a structural classification of proteins database
for the investigation of sequences and structures. J. Mol. Biol.
247, 536–540
|
| |
| 18. |
Holm, L. and Sander, C. (1997) Mapping the protein universe. Science
273, 595–602.
|
| |
| 19. |
Holm, L. and Sander, C. (1997) An evolutionary treasure: unification of a broad set of amiodhydrolases related to urease.
Proteins: Struct. Funct. Genet.
28, 72–82.
|
| |
| 20. |
Artymiuk, P. J., Poirette, A. R., Rice, D. W., and Willett, P. (1997) A polymerase I palm domain in adenylyl cyclase? Nature
388, 33–34.
|
| |
| 21. |
Orengo, C. A. (1994) Classification of protein folds. Curr. Opin. Struct. Biol.
4, 429–440.
|
| |
| 22. |
Holm, L. and Sander, C. (1994) Searching protein structure databases has come of age. Proteins: Struct. Funct. Genet.
19, 165–183.
|
| |
| 23. |
Holm, L. and Sander, C. (1997) New structure—novel fold? Structure
5, 165–171.
|
| |
| 24. |
Taylor, W. R. and Orengo, C. A. (1989) Protein structure alignment. J. Mol. Biol.
208, 1–22.
|
| |
| 25. |
Orengo, C. A., Brown, N. P., and Taylor W. R. (1992) Fast structure alignment for protein databank searching. Proteins: Struct. Funct. Genet.
14, 139–167
|
| |
| 26. |
Alexandrov, N. N., Takahashi, K., and Go, N. (1992) Common spatial arrangements of backbone fragments in homologous and non-homologous
proteins. J. Mol. Biol.
225, 5–9.
|
| |
| 27. |
Russell, R. B. and Barton, G. J. (1992) Multiple sequence alignment from tertiary structure comparison. Assignment of global
and residue confidence levels. Proteins: Struct. Funct. Genet.
14, 309–323.
|
| |
| 28. |
Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol.
233, 123–138.
|
| |
| 29. |
Holm, L. and Sander, C. (1994) The FSSP database of structurally aligned protein fold families. Nucleic Acids Res.
22, 3600–3609. See also Nucleic Acids Res.
24, 206–210.
|
| |
| 30. |
Mitchell, E. M., Artymiuk, P. J., Rice, D. W., and Willett, P. (1990) Use of techniques derived from graph theory to compare
secondary structure motifs in proteins. J. Mol. Biol.
212, 151–166.
|
| |
| 31. |
Quanta. Molecular Simulations, San Diego, CA.
|
| |
| 32. |
Gibrat, J.-F., Madej, T., Bryant, S. H. (1996) Surprising similarities in structure comparison. Curr. Opin. Struct. Biol.
6, 377–385.
|
| |
| 33. |
Kleywegt, G. J. and Jones, T. A. (1997) Detecting folding motifs and similarities in protein structures. Methods Enzymol.
277, 525–545.
|
| |
| 34. |
Russell, R. B. and Ponting, C. P. (1998) Protein fold irregularities that hinder sequence analysis. Curr. Opin. Struct. Biol.
8, 364.
|
| |
| 35. |
Murzin, A. G. (1998) Probable circular permutation in the flavin-binding domain. Nat. Struct. Biol.
5, 101.
|
| |
| 36. |
Liepinsh, E., Kitamura, M., Murakami, T., Nakaya, T., and Otting, G. (1997) Pathway of chymotrypsin evolution suggested by
the structure of the FMN-binding protein from Desulfovibrio vulgaris. Nat. Struct. Biol.
4, 975–979.
|
| |
| 37. |
Chothia, C. (1992) One thousand families for the molecular biologist. Nature
357, 543–544.
|
| |
| 38. |
Orengo, C. A., Jones, D. T., and Thornton, J. M. (1994) Protein superfamilies and domain superfolds. Nature
372, 631–634.
|
| |
| 39. |
Blundell, T. L. and Johnson, M. S. (1993) Catching the common fold. Protein Sci.
2, 877–883.
|
| |
| 40. |
Crippen, G. M. and Mariov, V. (1995) How many protein folding motifs are there? J. Mol. Biol.
252, 144–151.
|
| |
| 41. |
Russell, R. B., Saqi, M. A. S., Sayle, R. A., Bates, P. A., and Sternberg, M. J. E. (1997) Recognition of analogous and homologous
protein folds. Analysis of sequence and structure conservation. J. Mol. Biol.
269, 423–439.
|
| |
| 42. |
Jones, D. T. (1997) Progress in protein structure prediction. Curr. Opin. Struct. Biol.
7, 377–387.
|
| |
| 43. |
Murzin, A. G. (1993a) Sweet tasting protein monellin is related to the cystatin family of thiol proteinase inhibitors. J. Mol. Biol.
230, 689–694.
|
| |
| 44. |
Russell, R. B. and Barton, G. J. (1994) Structural features can be unconserved in proteins with similar folds. An analysis
of side-chain to side-chain contacts, secondary structure and accessibility. J. Mol. Biol.
244, 332–350.
|
| |
| 45. |
Holm, L. and Sander, C. (1997) Decision support system for the evolutionary classification of protein structures. Intel. Syst. Mol. Biol.
5, 140–146.
|
| |
| 46. |
Swindells, M. B. (1993) Classification of doubly wound nucleotide binding topologies using automated loop searches. Protein Sci.
2, 2146–2153.
|
| |
| 47. |
Murzin, A. G. (1995) A ribosomal protein module in EF-G and DNA gyrase, Nat. Struct. Biol.
2, 25–26.
|
| |
| 48. |
Holm, L. and Sander, C. (1995) DNA polymerase β belongs to an ancient nucleotidyltransferase superfamily. Trends Biochem. Sci.
20, 345–347.
|
| |
| 49. |
Holm, L. and Sander, C. (1997) An evolutionary treasure: unification of a broad set of amidohydrolases related to urease.
Proteins: Struct. Funct. Genet.
28, 72–82.
|
| |
| 50. |
Holm, L. and Sander, C. (1997) Enzyme HIT. Trends Biochem. Sci.
22, 116.
|
| |
| 51. |
Park J., Teichmann S. A., Hubbard T., and Chothia C. (1997) Intermediate sequences increase the detection of homology between
sequences. J. Mol. Biol.
273, 349–354.
|
| |
| 52. |
Russell, R. B., Saseini, P. D., and Sternberg, M. J. E. (1998) Supersites within superfolds. Binding site similarity in the
absence of homology. J. Mol Biol.
28, 903.
|
| |
| 53. |
Hol, W. G., van Duijnen, P. T., and Berendsen, H. J. (1978) The alpha-helix dipole and the properties of proteins. Nature
273. 443–446.
|
| |
| 54. |
Pennisi, P. (1998) Taking a structured approach to understanding proteins. Science
279, 978–979.
|
| |
| 55. |
Vrielink, A., Ruger, W., Driessen, H. P., Freemont, P. S. (1994) Crystal structure of the DNA modifying enzyme beta-glucosyltransferase
in the presence and absence of the substrate uridine diphosphoglucose. EMBO J.
13, 3413–3422
|
| |
| 56. |
Holm, L. and Sander, C. (1995) Evolutionary link between glycogen phosphorylase and a DNA modifying enzyme. EMBO J.
14, 1287–1293.
|
| |
| 57. |
Artymiuk, P. J., Rice, D. W., Poirette, A. R., and Willett, P. (1995) β-Glucosyltransferase and phophorylase reveal their
common theme, Nat. Struct. Biol.
2, 117–120.
|
| |
| 58. |
Zhang, G., Liu, Y., Ruoho, A. E., and Hurley, J. H. (1997) Structure of the adenylyl cyclase catalytic core. Nature
386, 247–253.
|
| |
| 59. |
Tesmer, J. J., Sunahara, R. K., Gilman, A. G., and Sprang, S. R. (1997) Crystal structure of the catalytic domains of adenylyl
cyclase in a complex with Gsα.GTPγS. Science
278, 1907–1916.
|
| |
| 60. |
Laskowski, R. A., Hutchinson, E. G., Michie, A. D., Wallace, A. C., Jones, M. L., and Thornton, J. M. (19??) PDBsum: a Web-based
database of summaries and analyses of all PDB structures. Trends Biochem. Sci.
22, 488–490.
|
| |
| 61. |
Wallace, A. C., Laskowski, R. A., and Thornton, J. M. (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand
interactions. Protein Eng.
8, 127–134.
|
| |
| 62. |
Schuler, G. D., Epstein, J. A., Ohkawa, H., and Kans, J. A. (1996) Entrez: molecular biology database and retrieval system
Methods Enzymol.
266, 141–162.
|
| |
| 63. |
Bryant, S. H., Madej, T., Janin, J., Liu, Y., Ruoho, A. E., Zhang, G., and Hurley, J. H. (1997) A polymerase I palm in adenylyl
cyclase? Nature
388, 34.
|
| |
| 64. |
Murzin, A. G. (1993b) Can homologous proteins evolve different enzymatic activities? Trends Biochem. Sci.
18, 403–405.
|
| |
| 65. |
Murzin, A. G. (1996) Structural classification of proteins: new superfamilies. Curr. Opin. Struct. Biol.
6, 386–394.
|
| |
| 66. |
Farber, G. K. and Petsko, G. A. (19??) The evolution of a/b barrel enzymes. Trends Biochem Sci
15, 228–234.
|
| |
| 67. |
Sayle, R. A. and Milner-White, E. J. (1995) RASMOL Biomolecular Graphics for all. Trends Biochem. Sci.
20, 374.
|
| |
| 68. |
Kraulis, P. J. (1991) Molscript: a program to produced detailed and schematic plots of protein structures. J. Appl. Cryst.
24, 946–950.
|
| |
| 69. |
Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. E., Brice, M. D., Rodgers, M. D., Kennard, O., Shimanouchi, T.,
and Tasumi, M. (1977) The Protein Data Bank: a computer-based archival file for macrormolecular structures. J. Mol. Biol.
112, 535–542.
|
| |