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Table 2. SCOP: Structural Classification of Proteins. 1.65 release (1-09-2003)
20619 PDB Entries, 54745 Domains (excluding nucleic acids and theoretical
models), http://scop.mrc-lmb.cam.ac.uk/scop/count.html
Class
Folds
Superfamilies
Families
All alpha proteins
179
299
480
All Beta proteins
126
234
462
a/b proteins
121
192
542
a+b proteins
234
330
567
Multi domain
38
39
53
Membrane and Cell surface
proteins
36
64
73
Small proteins
66
87
150
Total
800
1232
2327
Table 3. CATH, Version 2.5 (11-08-2003) 43229 domains.
http://www.biochem.ucl.ac.uk/bsm/cath/releases.html
C
A
T
H
S
Mainly alpha
5
228
433
957
Mainly beta
19
139
286
961
Alpha beta
12
361
659
2008
Few Secondary structures
1
85
89
110
Total
37
813
1503
4036
At the level of the fold there is more agreement between Dali and SCOP. CATH is the
outsider because of the broader range of structures encompassed by the CATH fold
definitions [55]. For example all the structures placed in the two most highly populated
folds in CATH, the Rossman fold and the immunoglobulin-like (Ig-like) fold, are also
found in the corresponding folds in Dali and SCOP although Dali and SCOP divide these
folds into a number of sub families. However the CATH Ig-like and Rossman folds also
contain structures that are not found in SCOP and Dali. Nevertheless there is a large
amount of agreement between the databases and it is possible to assign CATH and SCOP
classifications down to the topology and fold levels respectively from FSSP scores with a
high degree of success [56]. This may prove useful since the FSSP database is updated
more frequently than the other two.
5. Super-folds
Analysis of the CATH database has suggested that there is a limited number of protein
folds in nature estimated at one to several thousand [57] and, although there are topologies
yet to be sampled, it is evident that fold groups are not uniformly populated. In fact it has
been found that there is a bias towards 10 groups at the topology-level called super-folds,
which account for approximately one third of all the homologous superfamilies. The super-
