Throughout evolution, homologous proteins have common parts that stay semi-rigid relative to each other and other common ones that vary in a more noticeable way. In order to compare the increasing number of structures in the PDB, flexible geometrical alignments are needed, that be reliable and easy to use.
Here you find a protein structure alignment method whose main feature is the ability to consider different rigid transformations at different sites, allowing for deformations beyond a global rigid transformation.
It performs similar to Dali, Matras, Rash, TM-align, Vorolign, FatCat and others in a subset of Sisyphus, a handcured database, and also on the test of Sierk and Pearson based on CATH.
The use of a sequence of local transformations can be exported to most classifiers, and a future golden protein similarity measure could benefit from it.
J. Rocha; J. Segura; R. C. Wilson; S. Dasgupta : Flexible
structural protein alignment by a sequence of local transformations.
Bioinformatics, July, 2009; 25: 1625 - 1631. doi:
Kawabata, K. Nishikawa.
Protein Structure Comparison Using the
Markov Transition Model of Evolution. Proteins, 41, pp
108-122, 2000. (ProtDeform uses the code of Matras, specifically, the
Questions? jairo @at uib dot. es.