The CATH database is a hierarchical domain classification
of protein structures in the Protein Data Bank (PDB, Berman et al.
2003). Only crystal structures solved to resolution better than 4.0
angstroms are considered, together with NMR structures. All
non-proteins, models, and structures with greater than 30% "C-alpha
only" are excluded from CATH.
This
filtering of the PDB is performed using the SIFT protocol (Michie et
al., 1996). Protein structures are classified using a combination
of automated and manual procedures. There are four major levels in
this hierarchy: Class, Architecture, Topology
(fold family) and Homologous superfamily (Orengo etal., 1997). Each level is described below, together
with the methods used for defining domain boundaries and assigning
structures to a specific family.
Domain Boundary Assignments
All the classification is performed on individual protein domains.
To divide multidomain protein structures into their constituent
domains, a combination of automatic and manual techniques are used.
If a given protein chain has sufficiently high sequence identity and
structural similarity (ie. 80% sequence
identity, SSAP score >= 80) with a chain that has previously
been chopped, the domain boundary assignment is performed
automatically by inheriting the boundaries from the other chain
(ChopClose). Otherwise, the domain boundaries are assigned manually,
based on an analysis of results derived from a range of algorithms
which include structure based methods (CATHEDRAL, SSAP, DETECTIVE
(Swindells, 1995), PUU (Holm & Sander, 1994), DOMAK (Siddiqui and
Barton, 1995)), sequence based methods (Profile HMMs) and relevant
literature.
The CATH Hierarchy and Classification Procedures
Automated Procedures
If
a given domain has sufficiently high sequence and structural
similarity (ie. 35% sequence identity, SSAP score >= 80) with a
domain that has been previously classified in CATH, the
classification is automatically inherited from the other domain.
Otherwise, the domain is classified manually, based upon an analysis
of the results derived primarily from a range of comparison
algorithms CATHEDRAL, HMMs, SSAP scores and relevant literature.
Manual and Automated Procedures Combined
Class, C-level
Class is determined according to the secondary structure
composition and packing within the structure. Three major classes are
recognised; mainly-alpha, mainly-beta and alpha-beta. This last class
(alpha-beta) includes both alternating alpha/beta structures and
alpha+beta structures, as originally defined by Levitt and Chothia
(1976). A fourth class is also identified which contains protein
domains which have low secondary structure content.
Architecture, A-level
This describes the overall shape of the domain structure
as determined by the orientations of the secondary structures but
ignores the connectivity between the secondary structures. It is
currently assigned manually using a simple description of the
secondary structure arrangement e.g. barrel or 3-layer sandwich.
Reference is made to the literature for well-known architectures (e.g
the beta-propellor or alpha four helix bundle).
Topology (Fold family), T-level
Structures are grouped into fold groups at this level
depending on both the overall shape and connectivity of the secondary
structures. This is done using the structure comparison algorithm
SSAP (Taylor & Orengo, 1989) and CATHEDRAL (Harrison et al.
2002, 2003). Parameters for clustering domains into the same fold
family have been determined by empirical trials throughout the
databank (Orengo et al. 1992; Orengo et al. 1993;
Harrison et al. 2002, 2003). Structures which have a
SSAP score of 70 and where at least 60% of the larger protein matches
the smaller protein are assigned to the same T level or fold group.
Some fold fgroups are very highly populated (Orengo et
al. 1994); Orengo & Thornton, 2005)
particularly within the mainly-beta 2-layer sandwich
architectures and the alpha-beta 3-layer sandwich architectures.
Homologous Superfamily, H-level
This level groups together protein domains which are
thought to share a common ancestor and can therefore be described as
homologous. Similarities are identified either by high sequence
identity or structure comparison using SSAP. Structures are clustered
into the same homologous superfamily if they satisfy one of the
following criteria:
Sequence identity >= 35%, overlap >= 60% of larger structure equivalent to smaller.
SSAP score >= 80.0, sequence identity >= 20%, 60% of larger structure equivalent to smaller.
SSAP score >= 70.0, 60% of larger structure equivalent to smaller, and domains which have related functions, which is informed by the literature and Pfam protein family database, (Bateman et al., 2004).
Significant similarity from HMM-sequence searches and HMM-HMM comparisons using SAM (Hughey &Krogh, 1996), HMMER (http://hmmer.wustl.edu) and PRC (http://supfam.org/PRC).
Sequence Family Levels: (S,O,L,I, D)
Domains within each H-level are subclustered into
sequence families using multi-linkage clustering at the following
levels:
Level
Name
Sequence Identity Overlap
S
35%
80%
O
60%
80%
L
95%
80%
I
100%
80%
The D-level acts as a counter within each S100 family and
is appended to the classification hierarchy to ensure that every
domain in CATH has a unique CATHSOLID classification. The sequence
identity and overlap used for clustering are obtained from an
implementation of the Needleman-Wunsch algorithm (Needleman &
Wunsch, 1970) using a gap penalty of 3. The percentage sequence
identity is calculated as (100 * Number Of Identical Residues/Length
Of The Shortest Sequence) and the percentage overlap is calculated as
(100 * Number Of Aligned Residues/Length Of The Longest Sequence).
Class, C-level
Architecture, A-level
Topology (Fold family), T-level
Homologous Superfamily, H-level
Sequence Family Levels: (S,O,L,I, D)
