Description - PDB-REPRDB

Description
PDB-REPRDB : Representative protein chains from PDB

Method :

PDB-REPRDB is a reorganized database of protein chains from PDB. The protein chains are arranged in order of the quality of atomic coordinate data. Earliest chain is taken for a representative and compared with every other chain. Similar chains to the representative on

amino acid sequence or
structure similarity

are classified into the same group with the representative. The earliest chain in the rest ( not classified yet ) becomes the next representative.
Thus PDB-REPRDB supplies 'the list of the representative protein chains', unique to each other on sequence and structure, and 'the list of protein chain groups'.
For more information, see the document

References :

T. Noguchi, K. Onizuka, Y. Akiyama, and M. Saito:
"PDB-REPRDB: A Database of Representative Protein Chains in PDB (Protein Data Bank)".
Proc. of the Fifth International Conference on Intelligent Systems for Molecular Biology,
AAAI press (1997).

How to use :

Page 1 : Eliminate and Sort Chains

Select 'Apply constraints'.
Factors in the first column of this table determine the quality of atomic coordinates of protein chains in PDB.
Elimination and sort options make various data sets to be classified into groups afterward.
If you choose 'No' option for the apply constraints, as concerns the factor of this line, all the chains will be used. 'Yes' option causes elimination of chains by the following threshold.
Factors : "include MUTANT", "include COMPLEX" and "include NMR" are exceptions.
- include Mutant : If you choose 'Yes', chains of mutant will be used.
- include Complex : If you choose 'Yes', chains of complex will be used.
- include NMR : If you choose 'Yes', chains by NMR will be used.
Set 'threshold'.
- resolution : eliminate chains with greater value than the threshold
- r-factor : eliminate chains with greater value than the threshold
- number of chain break : eliminate chains with greater value than the threshold
- rate of non-standard amino acid residues : eliminate chains with greater value than the threshold
- rate of residues with only CA coordinates : eliminate chains with greater value than the threshold
- rate of residues with only backbone coordinates : eliminate chains with greater value than the threshold
- number of residues : eliminate chains with smaller value than the threshold
Set 'priority'.
Independently of elimination, chains are sorted by keys of factors.
At first, factor given '1' as priority is compared. Later factors are compared only after all earlier factor compare equal. Earlier chains have priority to be selected as representatives.
Push 'Reset this form' only if you want to reset the input form.
Then, push'Make List' button to extract and sort chains.

Page 2 : Select representative chains

See 'Service status' and check the service is ON.
Set the 'Parameters for classification'.

If you check the check-box of sequence similarity : ID%, chains whose ID% are over the threshold will be classified into the same group.
If you check the check-box of structure similarity : RMSD or Dmax, chains whose RMSD or Dmax are under the threshold will be classified into the same group.

Push 'Reset this form' only if you want to reset the input form.
Push 'Service status' button to confirm the service status for your query.
Then, push 'Submit' button to submit your query to the server.

PAPIA system,