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ProFunc   Prediction of protein function from 3D structure

The aim of the ProFunc server is to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses a series of methods, including fold matching, residue conservation, surface cleft analysis, and functional 3D templates, to identify both the protein's likely active site and possible homologues in the PDB.

From this page you can submit your own structure, analyse an existing PDB entry, or retrieve the results of a previously submitted run.

Choose option A, B or C:

A. Upload PDB-format file:
 
B. Use existing PDB file (4 chars):    Example: "5p21"
Runs ProFunc on an existing PDB entry or, if already done, takes you directly to the results page.
 
C. Go to previous analysis   Id no.:   Security code:

Some of the methods take minutes to run; others take hours. You will be notified by e-mail when the entire process is complete, but can check on preliminary results as they become available.

The files are usually stored for about 6 months before being deleted. However, they are stored on a partition that is not backed up; so, in principle, they could disappear at any time.

Notes

- Please try to limit the number of structures submitted to about 6 per hour to avoid overloading the server. To arrange a large batch run, please contact us.
- If your structure contains any non-standard amino acids (eg selenomethionines, phosphotyrosines, etc) it is a good idea to rename them in your PDB file to their closest standard equivalents. This will increase the chances of ProFunc finding matches to both sequence and structure templates. (For selenomethionines identified by residue name MSE there is no need to make any changes).
- For best results, please submit the coordinates of the complete 'biological unit', if known. If not known, you can use a server such as Pita or PISA to predict the likely quaternary structure (of an X-ray crystal structure).

 

 

ProFunc has been developed jointly with the Midwest Center for Structural Genomics (MCSG) spacer

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Related databases

PDBsum
Structural analyses of all PDB entries

Tempura
Customized 3D template generation from submitted structure and search vs PDB.