BioXGEM
.
3D-BLAST Download
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What's 3D-BLAST
Structural alphabet
Substitution matrix
E
-value
(
k
,
a
) map
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Standalone 3D-BLAST program
new!
You download the package from:
Standalone_3d-blast_Linux_beta102.tar.gz
After downloading the package to you Linux-based computer, uncompress it by following commands in terminal.
gunzip Standalone_3d-blast_Linux_beta102.tar.gz
tar -xpf Standalone_3d-blast_Linux_beta102.tar
And then, you may check the file "
README
" in the directory "Standalone_3d-blast_Linux" for more information about compilation and usage of 3D-BLAST.
Our experience of distributing 3D-BLAST is limited. Should you encounter any problems with download, installation, or execution, please do not hesitate to contact us.
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 29-May-10 (55MB)
nr-PDB-90 (9MB)
with Structural alphabet sequences
Auto-update every 2 weeks
SCOP
:
SCOP 1.75 (32MB)
SCOP 1.75 95% (5MB)
SCOP 1.75 40% (3MB)
with Structural alphabet sequences
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.