Fold matching using SSM
The SSM (Secondary Structure Matching)
program compares the fold of the given query structure
against the folds of the structures in the PDB. It uses a fast
graph-matching algorithm to identify possible matches based on the
secondary structure elements (SSEs) present in the two proteins being
For all potential hits a precise 3D alignment of C-alpha atoms is
performed, and hits are ranked according to the Z-scores computed from
the r.m.s.d. values obtained from these structural superpositions.
The link below explains the results shown by ProFunc for each
Key to results
Krissinel E and Henrick K (2004).
Secondary-structure matching (SSM), a new tool for fast protein structure
alignment in three dimensions
Acta Cryst., D60, 2256-2268.