IMAAAGINE: Search a hypothetical 3D protein arrangement in the Protein Data Bank.

The IMAAAGINE server is a protein structural motif database searching program.

Users can define an amino acid arrangment of 3 to 8 residues which will be converted into a search pattern. The search using the query is carried out against the PDB. 3D arrangements of amino acids in PDB structures that conform to the query will be returned to the user.

The IMAAAGINE server was designed as an interface and search engine to query PDB structures by utilising an understanding of the biochemical requirements for a particular function to generate a query. The server can also be used to identify novel structural motifs. IMAAAGINE searches the PDB using a graph theoretical approach. The core algorithm used has been reported for the searching of 3D base arrangements in complex RNA structures.

Citation for referencing IMAAAGINE:
Nurul Nadzirin, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2013. IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank. Nucleic Acids Res. 41 (W1): W432-W440. HTML, PDF.

To run a search:
1. Select the number of residues for the query pattern from the list below (3-8 residues).
2. Enter the specific residue or general type and set the distances between the residues.

Notes for setting up your search:
ALL residues must be connected as a whole, although not all distances need to be defined.
For distances that are not defined, a wildcard value is used during the search.
The distances entered will carry a variable tolerance value of (+/-)1.5 Angstroms.
Please see example searches for assistance.

Search times and output visualization:
1. Each search may take time to complete depending on the complexity of the query and the server load. Users are advised to bookmark the results page or copy the link to the results for analysis at a later point in time.
2. In order to use the output visualization features via Jmol, your web browser will need to be able to run Java. Please take note that there are known issues for Java 7 on the Chrome web browser for the Mac OSX operating system.
3. Search results will be kept for at least 2 days. The main search results can be downloaded to your local computer while still retaining the server side ability to view the hits in Jmol.

Please email for help or if you've detected any problems with the search.

Precomputed example:
1. Search for a "Ser-[D/E]-Ser-[D/E]-Ser-[D/E]" arrangement [See example]
2. Search for a four-Arginine cluster arrangement [See example]
3. Search for a pattern of two Asp-His-Ser triads [See example]

Demonstration search:
Click HERE to load a prefilled display of a "Ser-[D/E]-Ser-[D/E]-Ser-[D/E]" arrangement.

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