Searching a protein structure for 3D side chain arrangements of sites and motifs

SPRITE is a protein structural motif database searching program.

Users can upload a PDB file of a query protein structure, and SPRITE compares the input coordinates to a database of 3D side chain arrangements of sites and motifs using a graph theoretical approach.

In favorable cases, comparing 3D motifs may reveal biologically interesting similarities that are not detectable by comparing sequences or folds. The SPRITE search is independent of sequence order.

Citation for referencing SPRITE:
Nurul Nadzirin, Eleanor Gardiner, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2012. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W380-6. Epub 2012 May 9. HTML, PDF.

Notes: 
1. Please ensure that the query is a PDB formatted file.
2. Submitted searches may take a few minutes to complete, pease leave your browser on the page until the results are returned or use the link provided to retrieve the results. The program typically takes 1-5 minutes to complete depending on the size of your protein and the current server load. Thank you for your patience.
[see the Help page]

If your search query is a 3D motif or side chain arrangement to be searched against a structure database, please use the ASSAM program.

Upload a PDB file:

Or enter a 4-letter PDB ID: e.g., "4cha" or "4CHA"

Include 2-residue patterns? (Compulsory) No Yes
NOTE: Excluding 2-residue patterns is recommended.

* PDB input files will not be used for purposes other than the search and will be deleted after 2 days to a week upon search completion.

Demonstration run:
Click 'Submit' to do a demonstration SPRITE run :
4cha.pdb    [Submit]    Alpha-chymotrypsin
3tu8.pdb    [Submit]     Burkholderia Lethal Factor 1 (BLF1)
2oo2.pdb    [Submit]    Hypothetical protein AF_1782

Precomputed example:
View the precomputed results of a SPRITE search using:
4cha.pdb as input. [View]
3tu8.pdb as input. [View]
2oo2.pdb as input. [View]
 


SPRITE Pattern database statistics
Total searchable patterns = 3380

Pattern Dataset / Source
Number of patterns
Version
 
CSA
2628
4 Mar 2013
3D-Footprint
416
29 Apr 2013
ProCarb
206
Nov 2008
Others 130


MGI
Computational resources provided by the Genome Computing Centre, Malaysia Genome Institute


Please contact info_at_mfrlab.org ( _at_ = @ ) for any queries or to report errors.