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The C-alpha backbone structural comparison program was implemented by Daniel Fischer as part of his Ph.D. thesis research.
The current interface allows the user to specify 2 protein structures. These structures may be standard PDB structures or PDB format structures uploaded to our server. These protein's backbones are structurally compared using their c-alpha atoms coordinates. A set of high scoring conformations is output and the user may view these conformations in a PDB file viewer.
The structural matching is performed using geometric hashing, which allows the program to find structural matches that are indepenedent of the amino-acid sequence. The algorithm used, finds pairs of sub-structures from the two proteins that after under-going a rigid transformation will give the largest match possible.