How to use PAR-3D?

A query structure can be scanned for the motifs included in PAR-3D in the following manner.

• Step 1: Upload your own structure file in PDB format
• Step 2: Select the motif you want to search for
• Step 3: Press the upload button

The output of a typical PAR-3D search has been shown where PAR-3D identifies an unknown metal-binding site in the yeast YDR533c structure.



The output of a typical PAR-3D search has been described through result of 1TRN as the query structure.


The first line of the output describes the query protein's functional family. It is followed by a tabular description of the catalytic site predicted in the query structure. The first column of the table lists chain ID, second column indicates residue name and the third mentions the residue number of the catalytic site.

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