Kpax is a fast protein structure alignment and database search program. It uses Gaussian functions to score very rapidly the local and spatial environment of each amino acid residue in a protein, and it uses dynamic programming to find the optimal global alignment and superpositions of two proteins according to their Gaussian similarity scores. This approach allows very fast searches of structural databases, and it allows three-dimensional superpositions of proteins to be calculated rapidly.

New features: Kpax version 5.0.0 can perform flexible structure alignments, multiple structure alignments, and multiple flexible structure alignments. It can also score alignments calculated by other programs, provided the alignment is given in a PIR or FASTA format file.

Kpax was developed by Dave Ritchie.