Pairwise Protein Structure Alignment [more...]  [examples...]

Type PDB codes of the two molecules or upload files in PDB format:
Input Proteins PDB codes Chains (optional) Upload file
First Protein
Second Protein
Number of best matches

Fine tuning

Match precision: Coarse Standard Fine
Min. votes to qualify:

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 better results.

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.