About Tempura

Description

Tempura is a server designed to allow a user to specify the amino acids to be selected for searching using the "reverse template" approach previously published as part of the ProFunc suite. In addition to the selection of important residues, the user can also specify whether to search against a non-redundant representative sample of the PDB, an uploaded list of PDB codes (useful when examining specific families of proteins) or a single PDB code (for pairwise searches). Extensive use is made of the freely available RasMol molecular graphics program to view the molecules and their interactions in 3D (see additional links in documentation for instructions on the downloading and installation of RasMol.

Search

The Tempura server allows for two types of searches: either by uploading a 3D coordinate file or by entering the corresponding 4-character PDB code. Once a valid selection has been made or structure uploaded, a list of residues is presented for selection. Click on as many residues as required (use shift+click or ctrl+click for multiple residue selections) and then click "submit" to go to the database selection screen where the number of templates generated will be displayed.

There are then three database search options to choose from:

Non-redundant PDB - representative sample of the PDB culled at 30% sequence identity. Enter email address and click on the "NR PDB" button to continue.
Single PDB file - useful if looking to make a pairwise comparison and get a structural superposition based on local structural similarity. Enter the 4 character PDB code to be compared and user email address into the appropriate boxes. Click on "Get PDB ID" to continue.
List of PDB codes - useful if looking at a family of proteins or proteins from a single organism. User uploads a list of PDB codes they have constructed (a plain text file where each code is on a new line) using the browse button, enter user email address and click "upload list" to continue.

On successful completion, a message will be shown stating that the job has been submitted to the Tempura queue and will be processed soon. A link to the results is emailed to the address supplied when the run is complete.

Tempura publications

Latest reference

To be published

Related references

	Laskowski R A, Watson J D, Thornton J M (2005). Protein function prediction using local 3D templates. J. Mol. Biol., 351, 614-626. [PubMed id: 16019027]

	Laskowski R A, Watson J D, Thornton J M (2005). ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res., 33, W89-W93. Nucleic Acids Res., 33, W89-W93. [PubMed id: 15980588]

Credits

The Tempura server is derived from the "reverse template" analysis run as part of the ProFunc suite. This was created by:
Roman Laskowski, Janet Thornton
at the
European Bioinformatics Institute