CSA (Comparative Structural Alignment) is a webserver for computing and comparing protein structure alignments. CSA is able to compute score-optimal alignments with respect to various inter-residue distance-based scoring schemes.
I. Wohlers, N. Malod-Dognin, R. Andonov, G.W. Klau. CSA: comprehensive comparison of pairwise protein structure alignments. Nucleic Acids Res. (Web Server issue). 2012.
abstract: CSA is a web server for the computation, evaluation and comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue distance-based scorings of contact map overlap, PAUL, DALI and MATRAS. These and additional, uploaded alignments are compared using a number of quality measures and intuitive visualizations. CSA brings new insight into the structural relationship of the protein pairs under investigation and is a valuable tool for studying structural similarities.