A query structure can be scanned for 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
This program uses coordinates of residues and determines geometry in their structural context. Based on the geometry of the stored structural motifs, PAR-3D predicts the probable active site residues in the query protein structure. An example and description of how to use PAR-3D can be found here.
NOTE: A structure in PDB database can be searched by downloading the corresponding pdb file from RCSB on the local computer and then submitting to PAR-3D. Please go to RCSB and download the required query structure file.
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