DEDAL is a protein structure alignment tool which is independent of rigid-body constraints. This is carried out by systematically evaluating local structure context to identify similar regions of proteins. By focusing on local structure and performing a spatial rather than sequence attached analysis of matching substructures it is not constrained by any particular order of structural features along the protein sequence. Because it identifies all local similarities between compared structures, it offers a rigorous and complete analysis. It is also very conservative in not extending the structure-based sequence alignment, beyond regions of pronounced structure similarity.
P. Daniluk, B. Lesyng, A novel method to compare protein structures using local descriptors, BMC Bioinformatics 2011, 12:344
Daniluk, Paweł, and Bogdan Lesyng. Theoretical and Computational Aspects of Protein Structural Alignment. Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer Berlin Heidelberg, 2014. 557–598.