The c-alpha matching program was designed to find non-topological,
sequence independent similarities between protein structural motifs.
Enter the PDB code and chain ids (optionally) of the proteins you want to match.
Specify the number of possible matches you would like to see. Maximum 50.
You may use the fine-tuning parameters to get
When ready to go - press the Run the match button. Allow some time for
the program to run.
Matches will be presented, sorted by score. Best matches are presented
first. Bear in mind that in many cases the numerically favorable match is not
the one you're looking for. You'll have to do a little browsing.