DDBASE : (DIAL-derived domain database)
A database of Globular domains derived from non-redundant set of protein chains. This is usefull for the sequence analysis of aligned domains, for structural comparisions, for understanding domain stability and flexibility and for fold recognition procedures. Domains are defined by the program DIAL.
New Features
Statistics
Programs
References
Major changes made in DIAL program
Loop regions also considered for clustering
In this approach Secondary structures and Loops have been choped into
fixed residue size segments.
Helix 15 residue segment
Strand 10 residue segment
Loops 9 residue segment
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Total number of protein chains
Number of protein domains
Alpha class
Beta class
Alpha and Beta class
Few Secondary Structures(FSS)
multidomain proteins
single domain proteins
|
: 4151
: 6314
: 821
: 869
: 2806
: 1814
: 1641
: 2510
|
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SSTRUC
SSTRUC is a program to read in a Brookhaven format file and
to calculate torsions and seocondary structure assignments.
It was originally written by David Smith as a replacment for
the DSSP program of Kabsch and Sander.
DISMAT10
This program reads SSTRUC output and produces matrix of proximity indices for all possible segments
KITSCH2
This program clusters segments based on the
proximity indices. It was written by Joseph Felsenstein.
DISJOINT
program for identifying clusters from output of KITSCH2 program. This also claculates the Disjoint factor for all possible clusters and gives the table of possible Domain definition.
DANAL
This program creates PDB files corresponding to individual
domains and also creates subsidiary files which gives more information about domains including interdomain distance proximity.
Domains with lesser than 26 residues are made continuous with its contiguous domain.
Segments with lesser than 16 residues within a domain are combined to their contiguous segments occuring in any of the domains with the objective to reduce the number of discontinuous segments within a domain.
Modified entries are marked with red blinking star ()
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R.Sowdhamini & T.L.Blundell (1995).An automatic method involving cluster analysis of secondary structures for the identification of domains
in proteins. Prot. Sci., 4, 506-520.
R.Sowdhamini, S.D.Rufino & T.L.Blundell (1996). A database of globular
protein structural domains: clustering of representative family
members into similar folds. Folding and Design., 1, 209-220.
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