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J. Mol. Biol. (1995) 247, 536–540

COMMUNICATION

SCOP: A Structural Classification of Proteins Databasefor the Investigation of Sequences and Structures

Alexey G. Murzin, Steven E. Brenner, Tim Hubbard and Cyrus Chothia*

MRC Laboratory of Molecular To facilitate understanding of, and access to, the information available forprotein structures, we have constructed the Structural Classification ofBiology and Cambridge

Centre for Protein Proteins (scop) database. This database provides a detailed and com-prehensive description of the structural and evolutionary relationships ofEngineering, Hills Road

Cambridge CB2 2QH the proteins of known structure. It also provides for each entry links toco-ordinates, images of the structure, interactive viewers, sequence data andEnglandliterature references. Two search facilities are available. The homology searchpermits users to enter a sequence and obtain a list of any structures to whichit has significant levels of sequence similarity. The key word search finds, fora word entered by the user, matches from both the text of the scop databaseand the headers of Brookhaven Protein Databank structure files. Thedatabase is freely accessible on World Wide Web (WWW) with an entry pointto URL http://scop.mrc-lmb.cam.ac.uk/scop/

scop: an old English poet or minstrel (Oxford English Dictionary);

ckon: pile, accumulation (Russian Dictionary).

Keywords: protein families; superfamilies; folds; evolutionaryrelationships*Corresponding author

Nearly all proteins have structural similaritieswith other proteins and, in many cases, share acommon evolutionary origin. The knowledge ofthese relationships makes important contributions tomolecular biology and to other related areas ofscience. It is central to our understanding of thestructure and evolution of proteins. It will play animportant role in the interpretation of the sequencesproduced by the genome projects and, therefore, inunderstanding the evolution of development.

The recent exponential growth in the number ofproteins whose structures have been determined byX-ray crystallography and NMR spectroscopymeans that there is now a large and rapidly growingcorpus of information available. At present (January,1995) the Brookhaven Protein Databank (PDB,(Abola et al., 1987)) contains 3091 entries and thenumber is increasing by about 100 a month. Tofacilitate the understanding of, and access to, thisinformation, we have constructed the StructuralClassification of Proteins (scop) database. Thisdatabase provides a detailed and comprehensivedescription of the structural and evolutionaryrelationships of proteins whose three-dimensionalstructures have been determined. It includes all

proteins in the current version of the PDB andalmost all proteins for which structures have beenpublished but whose co-ordinates are not availablefrom the PDB.

The classification of protein structures in thedatabase is based on evolutionary relationships andon the principles that govern their three-dimensionalstructure. Early work on protein structures showedthat there are striking regularities in the ways inwhich secondary structures are assembled (Levitt& Chothia, 1976; Chothia et al., 1977) and in thetopologies of the polypeptide chains (Richardson,1976, 1977; Sternberg & Thornton, 1976). Theseregularities arise from the intrinsic physical andchemical properties of proteins (Chothia, 1984;Finkelstein & Ptitsyn, 1987) and provide the basis forthe classification of protein folds (Levitt & Chothia,1976; Richardson, 1981). This early work has beentaken further in more recent papers; see, for example,Holm & Sander (1993), Orengo et al. (1993),Overington et al. (1993) and Yee & Dill (1993). Anextensive bibliography of papers on the classificationand the determinants of protein folds is given in scop.

The method used to construct the proteinclassification in scop is essentially the visualinspection and comparison of structures thoughvarious automatic tools are used to make the taskmanageable and help provide generality. Given the

Abbreviations used: PDB, Protein Databank; scop,Structural Classification of Proteins.

0022–2836/95/140536–05 $08.00/0 7 1995 Academic Press Limited

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Figure 1. In scop, the unit of classification is usually theprotein domain. Small proteins, and most of those ofmedium size, have a single domain and are, therefore,treated as a whole. The domains in large proteins areusually classified individually. The protein entries in theDecember 1994 of the Brookhaven Protein Databank (PDB)contain 3179 domains. Many of these become forms of thesame protein whose differences are not significant in termsof the classification used here; for example they havedifferent bound ligands or engineered mutations. Todistinguish between these and structures of the sameprotein from different organisms, proteins listed within afamily are subclassified by species. Classification of the3179 domains show that they come from 498 families thatcan be clustered into 366 superfamilies and 279 differentfolds. In addition to these, scop contains entries for 195proteins that do not have atomic co-ordinates availablefrom the PDB at present but for which description of theirstructures have been published.

identities but whose functions and structures arevery similar; for example, globins with sequenceidentities of 15%.

SUPERFAMILY. Families, whose proteins havelow sequence identities but whose structures and, inmany cases, functional features suggest that acommon evolutionary origin is probable, are placedtogether in superfamilies; for example, actin, theATPase domain of the heat-shock protein andhexokinase (Flaherty et al., 1991).

COMMON FOLD. Superfamilies and families aredefined as having a common fold if their proteinshave same major secondary structures in samearrangement with the same topological connections.In scop we give for each fold short descriptions of itsmain structural features. Different proteins with thesame fold usually have peripheral elements ofsecondary structure and turn regions that differ insize and conformation and, in the more divergentcases, these differing regions may form half or moreof each structure. For proteins placed together in thesame fold category, the structural similaritiesprobably arise from the physics and chemistry ofproteins favouring certain packing arrangements andchain topologies (see above). There may, however,be cases where a common evolutionary origin isobscured by the extent of the divergence in sequence,structure and function. In these cases, it is possiblethat the discovery of new structures, with foldsbetween those of the previously known structures,will make clear their common evolutionary relation-ship.

CLASS. For convenience of users, the differentfolds have been grouped into classes. Most of thefolds are assigned to one of the five structural classeson the basis of the secondary structures of whichthey composed: (1) all alpha (for proteins whosestructure is essentially formed by a-helices), (2) allbeta (for those whose structure is essentially formedby b-sheets), (3) alpha and beta (for proteins witha-helices and b-strands that are largely inter-spersed), (4) alpha plus beta (for those in whicha-helices and b-strands are largely segregated) and(5) multi-domain (for those with domains of differentfold and for which no homologues are known atpresent). Note that we do not use Greek charactersin scop because they are not accessible to all worldwide web viewers. More unusual proteins, pep-tides and the PDB entries for designed proteins,

current limitations of purely automatic procedures,we believe this approach produces the mostaccurate and useful results. The unit of classifi-cation is usually the protein domain. Smallproteins, and most of those of medium size, havea single domain and are, therefore, treated as awhole. The domains in large proteins are usuallyclassified individually.

The classification is on hierarchical levels thatembody the evolutionary and structural relation-ships.

FAMILY. Proteins are clustered together intofamilies on the basis of one of two criteria that implytheir having a common evolutionary origin: first, allproteins that have residue identities of 30% andgreater; second, proteins with lower sequence

Table 1Facilities and databases to which SCOP has linksLink Source URL Reference

Co-ordinates PDB http://www.pdb.bnl.gov/ (Abola et al., 1987)Static images SP3D http://expasy.hcuge.ch/ (Appel et al., 1994)

gopher://pdb.pdb.bnl.gov/On-the-fly images NIH molecular http://www.nih.gov/www94/molrus (FitzGerald, 1994)

modelling groupSequences and NCBI Entrez http://www.ncbi.nlm.nih.gov/ (Benson et al., 1993)MEDLINE entries

The scop database contains links to a number of other facilities and databases in the world. Several interactive viewerscan be linked with scop using PDB co-ordinates. The location and nature of the links will vary as databases evolve andrelocate.

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Figure 2. A typical scop session is shown on a unix workstation. A scop page, of the Interleukin 8-like family, is displayedby the WWW browser program (NCSA Mosaic) (Schatz & Hardin, 1994). Navigating through the tree structure is accomplishedby selecting any underlined entry, by clicking on buttons (at the top of each page) and by keyword searching (at the bottomof each page). The static image comparing two proteins in this family was downloaded by clicking on the icon indicatedand is displayed by image-viewer program xv. By clicking on one of the green icons, commands were sent to a molecularviewer program (RasMol) written by Roger Sayle (Sayle, 1994), instructing it to automatically display the relevant PDB fileand colour the domain in question by secondary structure. Since sending large PDB files over the network can be slow,this feature of scop can be configured to use local copies of PDB files if they are available. Equivalent WWW browsers,image-display programs and molecular viewers are also available free for Windows-PC and Macintosh platforms.

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theoretical models, nucleic acids and carbohydrates,have been assigned to other classes.

The number of entries, families, superfamilies andcommon folds in the current version of scop areshown in Figure 1. The exact position of boundariesbetween family, superfamily and fold are, to somedegree, subjective. However, because all proteinsthat could conceivably belong to a family orsuperfamily are clustered together in the encom-passing fold category, some users may wish toconcentrate on this part of the database.

In addition to the information on structural andevolutionary relationships, each entry (for whichco-ordinates are available) has links to images of thestructure, interactive molecular viewers, the atomicco-ordinates, sequence data and homologues andMEDLINE abstracts (see Table 1).

Two search facilities are available in scop. Thehomology search permits users to enter a sequenceand obtain a list of any structures to which it hassignificant levels of sequence similarity. The keyword search finds, for a word entered by the user,matches from both the text of the scop database andthe headers of Brookhaven Protein Databankstructure files.

To provide easy and broad access, we have madethe scop database available as a set of tightly coupledhypertext pages on the world wide web (WWW).This allows it to be accessed by any machine on theinternet (including Macintoshes, PCs and work-stations) using free WWW reader programs, such asMosaic (Schatz & Hardin, 1994). Once such aprogram has been started, it is necessary only to‘‘open’’ URL:

http://scop.mrc-lmb.cam.ac.uk/scop/

to obtain the ‘‘home’’ page level of the database.In Figure 2 we show a typical page from the

database. Each page has buttons to go back to thetop-level home page, to send electronic mail to theauthors, and to retrieve a detailed help page.Navigating through the tree structure is simple;selecting any entry retrieves the appropriate page. Inaddition, buttons make it possible to move within thehierarchy in other manners, such as ‘‘upwards’’ toobtain broader levels of classification.

The scop database was originally created as atool for understanding protein evolution throughsequence-structure relationships and determining ifnew sequences and new structures are related topreviously known protein structures. On a moregeneral level, the highest levels of classificationprovide an overview of the diversity of proteinstructures now known and would be appropriateboth for researchers and students. The specific lowerlevels should be helpful for comparing individualstructures with their evolutionary and structurallyrelated counterparts. In addition, we have also foundthat the search capabilities with easy access to dataand images make scop a powerful general-purposeinterface to the PDB.

As new structures are released by PDB andpublished, they will be entered in scop and revised

versions of the database will be made available onWWW. Moreover, as our formal understanding ofrelationships between structure, sequence functionand evolution grows, it will be embodied inadditional facilities in the database.

Acknowledgements

We thank Sean Eddy, Graeme Mitchison and ErikSonnhammer for discussions and useful suggestions andRoger Sayle, the author of rasmol, for suggesting the tcl/tkinterface to rasmol. The University of Cambridge School ofBiological Sciences is providing the principal databaseaccess point. S.E.B. is grateful to Herchel Smith andHarvard University, St. John’s College, CambridgeOverseas Trust, American Friends of Cambridge Univer-sity and CVCP/ORS for support. T.H. is grateful toZENECA for support.

ReferencesAbola, E., Bernstein, F. C., Bryant, S. H., Koetzle, T. F. &

Weng, J. (1987). Protein Data Bank. In CrystallographicDatabases—Information Content, Software Systems,Scientific Applications (Allen, F. H., Bergerhoff, G. &Sievers, R., eds), pp. 107–132, Commission of theInternational Union of Crystallography, Bonn, Cam-bridge, Chester.

Appel, R. D., Bairoch, A. & Hochstrasser, D. F. (1994). Anew generation of information retrieval tools forbiologists: the example of the ExPASy WWW server.Trends Biochem. Sci. 19, 258–260.

Benson, D., Lipman, D. J. & Ostell, J. (1993). Genbank. Nucl.Acids Res. 21, 2963–2965.

Chothia, C. (1984). Principles that determine the structureof proteins. Annu. Rev. Biochem. 53, 537–572.

Chothia, C., Levitt, M. & Richardson, D. (1977). Structureof proteins: packing of a-helices and b-sheets. Proc.Nat. Acad. Sci., U.S.A. 74, 4130–4134.

Finkelstein, A. V. & Ptitsyn, O. B. (1987). Why do globularproteins fit the limited set of folding patterns. Prog.Biophys. Mol. Biol. 50, 171–190.

FitzGerald, P. C. (1994). A WWW Forms interface tofacilitate access (browsing, searching and viewing) ofthe molecular structure data contained within theBrookhaven Protein Data Bank (PDB). Proceedings ofWWW94 (First International Conference on the WorldWide Web), Chemistry Workshop, CERN, Geneva,Elsevier Science BV, Switzerland.

Flaherty, K. M., McKay, D. B., Kabsch, W. & Holmes, K. C.(1991). Similarity of the three-dimensional structuresof actin and the ATPase fragment of a 70 kDa heat shockcognate protein. Proc. Nat. Acad. Sci., U.S.A. 88,5041–5045.

Holm, L. & Sander, C. (1993). Protein structure comparisonby alignment of distance matrices. J. Mol. Biol. 233,123–138.

Levitt, M. & Chothia, C. (1976). Structural patterns inglobular proteins. Nature (London), 261, 552–558.

Orengo, C., Flores, T. P., Taylor, W. R. & Thornton, J. M.(1993). Identifying and classifying protein foldfamilies. Protein Eng. 6, 485–500.

Overington, J. P., Zhu, Z. Y., Sali, A., Johnson, M. S.,Sowdhamini, R., Louie, C. & Blundell, T. L. (1993).Molecular recognition in protein families: a databaseof three-dimensional structures of related proteins.Biochem. Soc. Trans. 21, 597–604.

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Richardson, J. S. (1976). Handedness of crossoverconnections in b-sheets. Proc. Nat. Acad. Sci., U.S.A. 73,2619–2623.

Richardson, J. S. (1977). b-Sheet topology and the related-ness of proteins. Nature (London), 268, 495–500.

Richardson, J. S. (1981). The anatomy and taxonomyof protein structure. Advan. Protein Chem. 34, 167–339.

Sayle, R. (1994). Rasmol. WWW, URL ftp://ftp.dcs.ed.ac.uk/rasmol.

Schatz, B. R. & Hardin, J. B. (1994). NCSA Mosaic and theworld wide web: global hypermedia protocols for theInternet. Science, 265, 895–901.

Sternberg, M. J. E. & Thornton, J. M. (1976). On theconformation of proteins: the handedness of theb-strand–a-helix–b-strand unit. J. Mol. Biol. 105,367–382.

Yee, D. P. & Dill, K. A. (1993). Families and the structuralrelatedness among globular proteins. Protein Sci. 2,884–899.

Edited by F. E. Cohen

(Received 1 November 1994; accepted 11 January 1995)