BioXGEM
.
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What's 3D-BLAST
Structural alphabet
Substitution matrix
E
-value
(
k
,
a
) map
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Structural Alphabet Sequence Database (SADB)
According to the
k
and
a
angles, each structure in the protein structure database has a specific
(
k
,
a
)-map distribution
and is able to be encoded into a corresponding 1D structural-alphabet sequence collected in the SADB database.
PDB
:
PDB (20-Jul-07)
nr-PDB-90
with
Structural alphabet sequences
Identifiers only
SCOP
:
SCOP 1.69
SCOP 1.69 95%
SCOP 1.69 40%
with
Structural alphabet sequences
Identifiers only
Pair database (674 pairs)
For coding structural alphabets and calculating the
SASM
.
SCOP-894
The SCOP-894 consists of 894 query proteins from two subsets, SCOP95-1.67 and SCOP95-1.69. The SCOP95-1.67 has 378 query proteins, which are in the SCOP 1.67 but not in the SCOP 1.65 and the search database is the SCOP 1.65. The SCOP95-1.69 consists of 516 query proteins, which are in SCOP 1.69 and not in SCOP 1.67 and the search database is the SCOP 1.67.
SG-319
The dataset consists of 319 proteins, which are selected from PDB and contributed by over 10 structural genomics consortia.
108 query domains
A diverse data set of 108 query domains proposed by Aung and Tan, Bioinformatics (2004) 20:1045-1052.
