Description - Protein Structure Similarity Search

Description
Protein Structure Similarity Search
for 3-D coordinates

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.
Input any label for your query into 'Query label=' field.

Input your 3-D coordinates of C-alpha carbons.
Format : (x-coordinate) (y-coordinate) (z-coordinate)
Example :

26.369	-3.226	33.623
23.790	-0.436	34.202
25.876	2.545	35.287
22.640	4.524	35.922

For convenience, so-called PDB ATOM lines are also accepted.
Then, each line should start with 'ATOM' label.
Only 'Ca' (C-alpha carbon) line will be read. Other ignored.
Example :

ATOM     45  N   GLU    53      18.222  18.496 -16.203  1.00 21.95      1CTF  95
ATOM     46  CA  GLU    53      17.706  17.982 -14.905  1.00 16.74      1CTF  96
ATOM     47  C   GLU    53      17.368  16.466 -15.121  1.00 15.45      1CTF  97
ATOM     48  O   GLU    53      16.780  16.073 -16.175  1.00 18.81      1CTF  98
ATOM     49  CB  GLU    53      16.552  18.744 -14.351  1.00 17.35      1CTF  99

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,