This option will search the PDB for similar structure/folds to the query protein. You can search by the whole protein, a selection or non-contiguous selection (e.g. ligand binding pocket).

• First read in your query protein structure.
• Next select the whole protein, a selection or non-contiguous s election (e.g. ligand binding pocket).
• You can then right click and choose "3D protein similarity search" or select it in the Tools menu.
• A dialog box will be displayed and there is an option to update PDB index. First update your index - it might take a few minutes.
• Then select the rmsd search threshold - ICM will not report any hits higher than the threshold
• Click OK to run the search.
• A table will then be displayed reporting the hits ranked by rmsd.
• Double click to load the structure and superimpose it onto your query protein.