Description - Protein Structure Similarity Search

Description
Protein Structure Similarity Search
for a protein fragment in PDB-REPRDB

Method :

Kabsch's method (rigorous calculation of RMSD). Query fragment is compared to all possible fragments in the protein chains registered in PDB-REPRDB database. No gap assumed in aligning two fragments. At first, the query fragment is rotated so that the RMSD (Root-Mean-Square Distance) between the query and a candidate fragment is minimized. Then RMSD value is calculated. In order to reduce output, RMSD threshold or Dmax (max distance between corresponding atom pairs in matching) threshold can be specified.

References :

W. Kabsch: "A discussion of the solution for the best rotation to relate two sets of vectors",
Acta Cryst. A34, pp.827-828 (1978).

How to use :

See 'Service status' and confirm the service is ON.
Select 'Database'.
You can only select PDB-REPRDB ( representative chain from PDB ) at the moment.
Set 'Search Threshold'.
Select 'Sorted by RMSD' or 'Sorted by Dmax'.
- RMSD : the Root mean square deviation between the query and the structure
- Dmax : the maximal distance between the corresponding Atoms
Put appropriate values in upper and lower threshold fields.
( You cannot omit both upper and lower at a time. )
Set 'Max. Output Number'.
The output will be truncated by this number.
Maximum number is 300.
Set 'PDB-REPRDB entry'.
Enter PDB Entry ID code and Chain-ID code into each field.
Indicate the region of the fragment by setting 'from' field and 'to' field with residue number.
Push 'Service status' button to confirm the service status for your query.
Push 'Reset this form' only if you want to reset the input form.
Then, push 'Submit' button to submit your query to the server.
Results Example

PAPIA system,