ProMatch is an algorithm for pairwise protein structure alignment developed by Aleksandar Poleksic at the University of Northern Iowa. The algorithm is specifically designed to detect structural relationships between proteins that exhibit complex structural modifications, such as large residue insertions and deletions, large conformational variations and circular permutations.
The algorithm builds upon our previously published method for computing superpositions that rigorously optimize the bottleneck distance measure, which represents the number of residues in two proteins that can be fit under a predefined distance cutoff (Poleksic, 2009). To address a variety of possible structural modification, ProMatch incorporates techniques for detecting domain swaps and circular permutations and conformational variations, such as those that occur upon ligand binding.
Poleksic,A. (2009) Algorithms for optimal protein structure alignment. Bioinformatics, 25, 2751-2756.