Use this when the structure isn't registered in 3decision, for example a model you just built. For a registered structure, start from the Workspace instead: see How to find pockets similar to a binding site.
Prerequisites: a structure file in .pdb, .cif or .mmCIF format.
- On the Home page, click Pocket Similarity From File.
- Upload Structure: drag the file into the page, or click to browse. Click Next.
- Select Residues: enter the residues that define the query pocket. Check them in the 3D viewer. Click Next.
- Select Parameters: check the settings and filters. They are the same as in the Workspace search panel.
- Start the search.
Result: the hits appear in a Pocket Search collection in the Workspace.