This article describes calculating multiple flexible alignments and the new "M-score" for scoring multiple alignments:

• Calculating and scoring high quality multiple flexible protein structure alignments. D.W. Ritchie (2016). Bioinformatics, and Supplementary Material.

This article describes the original Kpax pair-wise structure alignment algorithm:

• Fast Protein Structure Alignment using Gaussian Overlap Scoring of Backbone Peptide Fragment Similarity. D.W. Ritchie, A.W. Ghoorah, L. Mavridis, V. Venkatraman (2012). Bioinformatics, 28(24) 3274-3281, and Supplementary Material.

We thought that Kpax was a cool name for our program. But it turns out we were not the first! Here is a paper describing "kPax":

• Bayesian search of functionally divergent protein subgroups and their function specific residues. P. Marttinen, J. Corander, P. Toronen, L. Holm (2006). Bioinformatics, 22, 2466-2474.
• The Other K-Pax

So just for completeness, here are some further references:

• K-PAX (the novel), by Gene Brewer, first published by St. Martin's Press, New York (1995).
• K-PAX (the movie), starring Kevin Spacey and Jeff Bridges, directed by Iain Softley (2001).
• K-trivia, in case you ever wondered about US radio station call-letters.

Here are some links to lists of other protein structure alignment programs:

• Wikipedia Structural Alignment Software
• Gene Infinity Web Bench