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For a multiple sequence alignment which is based on a multiple structure alignment use a newly available method STACCATO (currently available only for download).
MultiProt Download (for Linux OS only)
Multiple Protein Structure Alignment
protein structural alignment
protein structure comparison
protein structural comparison
MultiProt is a fully automated highly efficient technique which detects the multiple structural alignments of protein structures. It finds the common geometrical cores between the input molecules. Most of the existing methods require that all the input molecules be aligned, while MultiProt does not require that all the input molecules participate in the alignment. Actually, it efficiently detects high scoring partial multiple alignments for all possible number of molecules from the input.
The final structural alignment can either preserve the sequence order (like sequence alignment), or be sequence order independent.
Shatsky, M. and Nussinov, R. and Wolfson, H.J., A method for simultaneous alignment of multiple protein structures. Proteins: Structure, Function, and Bioinformatics. 2004 Jul 1;56(1):143-56.