Task 6 : Kpax – Very Fast Protein Structure Alignment Algorithm


Kpax is a fast protein structure database search and alignment 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 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.

  • Based on Needleman-Wunsch, with Gaussian overlap scores
  • Can search ∼11,000 CATH structures in about 6 seconds...


Algorithm and Examples




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