Structural databases in use

The databases in use for Yakusa are made up of structures sharing variable amino acid sequence identities (from 20% to 95%). Depending on the particular database (see below), several algorithms can be used for sequence comparisons, the structure group representative can be chosen in several way and proteic structures can be cut up into domains; therefore

ASTRAL databases

The ASTRAL databases are partially derived from protein structures and their sequences.

ASTRAL 40: ASTRAL SCOP 1.65 genetic domain sequence subsets, based on PDB SEQRES records,with less than 40% identity to each other.
ASTRAL 95: ASTRAL SCOP 1.65 genetic domain sequence subsets, based on PDB SEQRES records,with less than 95% identity to each other.

PDB CLUSTER50,70,90 databases

The cluster databases are derived from protein structures and their sequences. These clusters are delivered within PDB mirror (in pdb/derived_Yakusa/data/NR sub=directory). Note: The file that contains nucleic acid chains and short polypeptides of fewer than 20 amino acids are not clustered.

CLUSTER 50: structures having less than 50% sequence identity to each other.
CLUSTER 70: structures having less than 70% sequence identity to each other.
CLUSTER 90: structures having less than 90% sequence identity to each other.

CULLING databases (PISCES)

For example,"CULLING database 20% identity resolution 1.6A R=0.25" contains PDB structures with

less than 20% sequence identity,
minimum X-RAY resolution of 1.6A,
a R-factor cutoff of 0.25.

Our database

In order to get accurate results and to limit an uninteresting huge output, we use a non redundant PDB, made up of protein structures which:

are made up of only one PDB chain,
do not share more than 80% identities in amino-acid sequences,
have more than 80 residues.

Search if a structure is in our database or in CLUSTER 50/79/90

Last modified: Wed Dec 1 17:16:08 CET 2004

Choose your database:
Four letters PDB code (example: 2hpd):
Now ... or...