International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

© International Union of Crystallography 2006
International Tables for Crystallography (2006). Vol. F. ch. 23.1, pp. 575-578   | 1 | 2 |
https://doi.org/10.1107/97809553602060000714

Chapter 23.1. Protein folds and motifs: representation, comparison and classification

C. Orengo,a J. Thornton,d L. Holmb and C. Sanderc

a Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1E 6BT, England,bEMBL–EBI, Cambridge CB10 1SD, England,cMIT Center for Genome Research, One Kendall Square, Cambridge, MA 02139, USA, and dBiochemistry and Molecular Biology Department, University College London, Gower Street, London WC1E 6BT, England, and Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, England

References

First citation Abola, E. E., Bernstein, F. C., Bryant, S. H., Koetzle, T. F. & Weng, J. (1987). Protein Data Bank. In Crystallographic databases – information content, software systems, scientific applications, edited by F. H. Allen, G. Bergerhoff, & R. Sievers, pp. 107–132.Google Scholar
 First citation Artymiuk, P. J., Mitchell, E. M., Rice, D. W. & Willett, P. (1989). Searching techniques for databases of protein structures. J. Inf. Sci. 15, 287–298.Google Scholar
 First citation Artymiuk, P. J., Rice, D. W., Poirrette, A. R. & Willett, P. (1995). Beta-glucosyltransferase and phosphorylase reveal their common theme. Nature Struct. Biol. 2, 117–120.Google Scholar
 First citation Barton, G. J. (1997). 3Dee: database of protein domain definitions. http://barton.ebi.ac.uk/servers/3Dee.html .Google Scholar
 First citation Bennett, M. J. & Eisenberg, D. (1994). Refined structure of monomeric diphtheria toxin at 2.3 Å resolution. Protein Sci. 3, 1464–1475.Google Scholar
 First citation Bork, P. (1992). Mobile modules and motifs. Curr. Opin. Struct. Biol. 2, 413–421.Google Scholar
 First citation Brenner, S. E., Chothia, C., Hubbard, T. J. & Murzin, A. G. (1996). Understanding protein structure. Using SCOP for fold interpretation. Methods Enzymol. 266, 635–643.Google Scholar
 First citation Brown, N. P., Orengo, C. A. & Taylor, W. R. (1996). A protein structure comparison methodology. Comput. Chem. 20, 359–380.Google Scholar
 First citation Chothia, C. (1993). One thousand families for the molecular biologist. Nature (London), 357, 543–544.Google Scholar
 First citation Crippen, G. (1978). The tree structural organization of proteins. J. Mol. Biol. 126, 315–332.Google Scholar
 First citation Flores, T. P., Orengo, C. A. & Thornton, J. M. (1993). Conformational characteristics in structurally similar protein pairs. Protein Sci. 7, 31–37.Google Scholar
 First citation Gibrat, J. F., Madej, T., Spouge, J. L. & Bryant, S. H. (1997). The VAST protein structure comparison method. Biophys. J. 72, MP298.Google Scholar
 First citation Go, M. (1981). Correlation of DNA exonic regions with protein structural units in hemoglobin. Nature (London), 291, 90–92. Google Scholar
 First citation Hogue, C. W., Ohkawa, H. & Bryant, S. H. (1996). A dynamic look at structures: WWW-Entrez and the molecular modelling database. Trends Biochem. Sci. 21, 226–229.Google Scholar
 First citation Holm, L. & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123–138.Google Scholar
 First citation Holm, L. & Sander, C. (1994a). Searching protein structure databases has come of age. Proteins, 19, 165–173.Google Scholar
 First citation Holm, L. & Sander, C. (1994b). Parser for protein folding units. Proteins, 19, 256–268.Google Scholar
 First citation Holm, L. & Sander, C. (1995). Evolutionary link between glycogen phosphorylase and a DNA modifying enzyme. EMBO J. 14, 1287–1293.Google Scholar
 First citation Holm, L. & Sander, C. (1996). Mapping the protein universe. Science, 273, 595–602.Google Scholar
 First citation Holm, L. & Sander, C. (1997). Enzyme HIT. Trends Biochem. Sci. 22, 116–117.Google Scholar
 First citation Holm, L. & Sander, C. (1998). Dictionary of recurrent domains in protein structures. Proteins, 33, 88–96.Google Scholar
 First citation Holm, L. & Sander, C. (1999). Protein folds and families: sequence and structure alignments. Nucleic Acids Res. 27, 244–247.Google Scholar
 First citation Islam, S. A., Luo, J. & Sternberg, M. J. (1995). Identification and analysis of domains in proteins. Protein Eng. 8, 513–525.Google Scholar
 First citation Jones, S., Stewart, M., Michie, A. D., Swindells, M. B., Orengo, C. A. & Thornton, J. M. (1998). Domain assignment for protein structures using a consensus approach: characterisation and analysis. Protein Sci. 7, 233–242.Google Scholar
 First citation Kikuchi, T., Nemethy, G. & Scheraga, H. A. (1988). Prediction of the location of structural domains in globular proteins. J. Protein Chem. 88, 427–471.Google Scholar
 First citation Kraulis, P. J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946–950.Google Scholar
 First citation Lesk, A. M. & Rose, G. D. (1981). Folding units in globular proteins. Proc. Natl Acad. Sci. USA, 78, 4304–4308.Google Scholar
 First citation Levitt, M. & Chothia, C. (1976). Structural patterns in globular proteins. Nature (London), 261, 552–558.Google Scholar
 First citation Li, M., Dyda, F., Benhar, I., Pastan, I. & Davies, D. R. (1996). Crystal structure of the catalytic domain of Pseudomonas exotoxin A complexed with a nicotinamide adenine dinucleotide analog: implications for the activation process and for ADP ribosylation. Proc. Natl Acad. Sci. USA, 93, 6902–6906.Google Scholar
 First citation Lionetti, C., Guanziroli, M. G., Frigerio, F., Ascenzi, P. & Bolognesi, M. (1991). X-ray crystal structure of the ferric sperm whale myoglobin: imidazole complex at 2.0 Å resolution. J. Mol. Biol. 217, 409–412.Google Scholar
 First citation Mizuguchi, K., Deane, C. A., Blundell, T. L. & Overerington, J. P. (1998). HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci. 7, 2469–2471.Google Scholar
 First citation Moult, J. & Unger, R. (1991). An analysis of protein folding pathways. Biochemistry, 30, 3816–3824.Google Scholar
 First citation Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. (1995). SCOP: a structural classification of the protein database for the investigation of sequences and structures. J. Mol. Biol. 247, 536–540.Google Scholar
 First citation Nemethy, G. & Scheraga, H. A. (1979). A possible folding pathway of bovine pancreatic Rnase. Proc. Natl Acad. Sci. USA, 76, 6050–6054.Google Scholar
 First citation Orengo, C. A., Jones, D. T., Taylor, W. & Thornton, J. M. (1994). Protein superfamilies and domain superfolds. Nature (London), 372, 631–634.Google Scholar
 First citation Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B. & Thornton, J. M. (1997). CATH – a hierarchic classification of protein domain structures. Structure, 5, 1093–1108.Google Scholar
 First citation Orengo, C. A., Pearl, F. M. G., Bray, J. E., Todd, A. E., Martin, A. C., LoConte, L. & Thornton, J. M. (1999). The CATH database provides insights into protein structure/function relationships. Nucleic Acids Res. 27, 275–279.Google Scholar
 First citation Phillips, D. E. (1970). British biochemistry, past and present, p. 11. London Biochemistry Society Symposium. Academic Press.Google Scholar
 First citation Rashin, A. A. (1976). Location of domains in globular proteins. Nature (London), 291, 85–87.Google Scholar
 First citation Richardson, J. S. (1981). The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34, 167–339.Google Scholar
 First citation Rose, G. D. (1979). Hierarchic organization of domains in globular proteins. J. Mol. Biol. 134, 447–470.Google Scholar
 First citation Rossmann, M. G. & Argos, P. (1975). A comparison of the heme binding pocket in globins and cytochrome b5. J. Biol. Chem. 250, 7525–7532.Google Scholar
 First citation Rossmann, M. & Liljas, A. (1974). Recognition of structural domains in globular proteins. J. Mol. Biol. 85, 177–181.Google Scholar
 First citation Russell, R. B. & Barton, G. J. (1993). Multiple protein sequence alignment from tertiary structure comparisons. Assignments of global and residue level confidences. Proteins, 14, 309–323.Google Scholar
 First citation Sali, A. & Blundell, T. B. (1990). The definition of general topological equivalences in proteins: a procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J. Mol. Biol. 212, 403–428.Google Scholar
 First citation Sander, C. (1981). Physical criteria for folding units of globular proteins. In Structural aspects of recognition and assembly in biological macromolecules, Vol. I. Proteins and protein complexes, fibrous proteins, edited by M. Balaban, pp. 183–195. Jerusalem: Alpha Press.Google Scholar
 First citation Sander, C. & Schneider, R. (1991). Database of homology-derived protein structures and structural meaning of sequence alignments. Proteins, 9, 56–68.Google Scholar
 First citation Schulz, G. E. & Schirmer, H. (1979). Principles of protein structure, ch. 5. New York: Springer Verlag.Google Scholar
 First citation Siddiqui, A. S. & Barton, G. J. (1995). Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions. Protein Sci. 4, 872–884.Google Scholar
 First citation Sowdhamini, R., Rufino, S. D. & Blundell, T. L. (1996). A database of globular protein structural domains: clustering of representative family members into similar folds. Structure Fold. Des. 1, 209–220.Google Scholar
 First citation Swindells, M. B. (1995). A procedure for detecting structural domains in proteins. Protein Sci. 4, 103–112.Google Scholar
 First citation Taylor, W. R. & Orengo, C. A. (1989). Protein structure alignment. J. Mol. Biol. 208, 1–22.Google Scholar
 First citation Tormo, J., Lamed, R., Chirino, A. J., Morag, E., Bayer, E. A., Shoham, Y. & Steitz, T. A. (1996). Crystal structure of a bacterial family-III cellulose-binding domain: a general mechanism for attachment to cellulose. EMBO J. 15, 5739–5751.Google Scholar
 First citation Vriend, G. & Sander, C. (1991). Detection of common three-dimensional substructures in proteins. Proteins, 11, 552–558.Google Scholar
 First citation Wernisch, L., Hunting, M. & Wodak, J. (1999). Identification of structural domains in proteins by a graph heuristic. Proteins, 35, 338–352.Google Scholar
 First citation Wetlaufer, D. B. (1973). Nucleation, rapid folding, and globular intrachain regions in proteins. Proc. Natl Acad. Sci. USA, 70, 697–701.Google Scholar
 First citation Wodak, J. & Janin, J. (1981). Location of structural domains in proteins. Biochemistry, 20, 6544–6552.Google Scholar
 First citation Zehfus, M. H. (1994). Binary discontinuous compact protein domains. Protein Eng. 7, 335–340.Google Scholar
 First citation Zehfus, M. H. (1997). Identification of compact, hydrophobically stabilized domains and modules containing multiple peptide chains. Protein Sci. 6, 1210–1219.Google Scholar
 First citation Zehfus, M. H. & Rose, G. D. (1986). Compact units in proteins. Biochemistry, 25, 5759–5765.Google Scholar