Triangle Match - Pairwise Protein Structure Alignment

The C-alpha backbone structural comparison program was implemented by Daniel Fischer as part of his Ph.D. thesis research.

The user inputs 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.

You may download the program - see the link above .
Once you download, you will be able to run the program in a few variations.
The readme file describes how to run one pdb against a set of pdbs.

Bibliography

• Bachar, O. and Fischer, D. and Nussinov, R. and Wolfson, H.J.,
  A Computer Vision Based Technique for 3-D Sequence Independent Structural Comparison of Proteins,
  Protein Engineering, Vol. 6, No. 3. pp. 279-288, 1993
• Fischer, D. and Bachar, O. and Nussinov, R. and Wolfson, H.J.,
  An Efficient Automated Computer Vision Based Technique for Detection of Three Dimensional Structural Motifs in Proteins,
  J. Biomolec. Struct. and Dyn. vol. 9, no. 4, pp. 769-789, 1992.