ProtDeform: Protein Structural Alignment

ProtDeform in Action!

Protein A:

Protein B:

Just press Submit to see a demo that aligns the ribosomal protein L1 mutant S179C [SCOP code d1ad2] and the 50S ribosomal protein LIP from Methanococcus jannaschii [SCOP code d1cjsa].
Or upload your own pdb files.

Local Deformations

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.

Download the program

Additional Material


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: 10.1093/bioinformatics/btp296 . (Link)

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 first classifier).

Questions? jairo @at uib dot. es.