Comparison Tool for Exploring Sequence and Structure Alignments
RCSB PDB's Comparison Tool calculates pairwise sequence (blast2seq, Needleman-Wunsch, and Smith-Waterman) and structure alignments (FATCAT, CE, TM-Align, TopMatch, Dali).
Comparisons can be made for any protein in the PDB archive and for customized or local files not in the PDB. Special features include support for both rigid-body and flexible alignments (via jFATCAT) and circular permutations that are difficult for many alignment algorithms to detect (via jCE).
The Comparison Tool is also integrated with the Sequence Clusters offered from each entry's Sequence Similarity tab. Users can select a pair of chains from a given sequence cluster (with similarity cutoffs of 100%, 95%, 90%, 70%, 50%, 40%, or 30%) and run alignment comparisons.
Documentation and acknowledgements are available from the Compare Structures page.