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Superfamilies
Families
(2) Folds:
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All alpha proteins
All beta proteins
Alpha and beta proteins (α
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β) Mainly parallel beta
sheets (beta-alpha-beta units)
Alpha and beta proteins (α
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Mainly antiparallel beta sheets (segregated alpha and
beta regions)
Multi-domain proteins (alpha and beta)
Folds consisting of two or more domains belonging to
different classes
Membrane and cell surface proteins and peptides
Does not include proteins in the immune system
Small proteins
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disulfide bridges
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Proteins are defined as having a common fold if they have the
same major secondary structures in the same arrangement and
with the same topological connections
(3) Superfamily: &
Proteins that have low sequence identities, but whose structural
and functional features suggest that a common evolutionary
origin is probable are placed together in superfamilies
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Proteins clustered together into families are clearly evolutionarily
related. Generally, this means that pairwise residue identities
between the proteins are 30% and greater
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Database of 498 SCOP “Folds” or “Superfamilies”
The overall pair-wise comparisons of 498 folds lead to a 498 x 498 matrix of
similarity scores Sijs, where Sij is the alignment score between the ith and jth folds.
An appropriate method for handling such data matrices as a whole is metric matrix
distance geometry. The similarity score matrix [Sij] is first converted to a distance
matrix [Dij] by using Dij = Smax - Sij, where Smax is the maximum similarity score
among all pairs of folds.
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= 7
The distance matrix is then transformed to a metric (or Gram) matrix [Mij] by using
Mij = Dij2 - Dio2 - Djo2
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where Di0, the distance between the ith fold and the geometric centroid of all N =
498 folds. The eigen values of the metric matrix define an orthogonal system of
axes, called factors. These axes pass through the geometric centroid of the points
representing all observed folds and correspond to a decreasing order of the
amount of information each factor represents.
B
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Nucleic Acids Research, 2003, Vol. 31, No. 13, 3386-3392
Nucleic Acids Research, 2003, Vol. 31, No. 13, 3386-3392
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