Proteins to be aligned
Please select input type (PDB/file) for each entry and press the update button.
Individual protein chains can be selected entering the chain index after the PDBid: 1aidA will select chain A of PDB entry 1aid

1. PDB codefile upload remove entry
2. PDB codefile upload remove entry

Parameters Energy interaction range (A) (0.1 - 12.0):
Tolerance for alignment (A) (0.1 - 12.0):
Shortest aligned segment (A) (1 - 100) :
Allow sequence inversion yes no


This webserver implements the energy-based multiple protein structural alignment method described in ref. 1. You can submit alignments involving up to 20 proteins. Protein length is limited to 500 amino acids. If you plan to run alignments involving more, or longer, proteins you can run MISTRAL on your local machine. To obtain the MISTRAL executable (free of charge for academic use) please contact the authors: michelet _at_ sissa.it or henri.orland _at_ cea.fr .

Input and output formats

Your input should be provided in PDB format. Upon successful completion of the job you will be directed to a results page containing:

1. detailed output regarding the alignment: alignment energy, core size, RMSD, sequence identity (sid), z-score and p-value. Note that the z-score and p-values are provided ONLY for pairwise alignments carried out with the default energy interaction range (8A);
2. a link to a PDB file combining the aligned input proteins (separated by the "MODEL" tag). Aligned amino acids have a non-zero entry in the B-factor column;
3. a link to a text file containing the list of corresponding residues.


1. C. Micheletti and H. Orland, MISTRAL: a tool for energy-based multiple structural alignment of proteins, Bioinformatics, vol. 25, p. 2663-2669 (2009). Link to article


To report errors in accessing the webserver please contact: Anne.Capdepon _at_ cea.fr .