Section: New Software and Platforms

Kpax

Keywords: Protein Structure Alignment

Scientific Description

Kpax is a program for flexibly aligning two or more protein structures and for searching databases of protein structures.

Functional Description

The Kpax program exploits the fact that each amino acid residue has a carbon atom with a highly predictable tetrahedral geometry. This allows the local environment of each residue to be transformed into a canonical orientation, thus allowing easy comparison between the canonical orientations of residues within pairs of proteins using a novel scoring function based on Gaussian overlaps. Kpax is now used by the KBDOCK web server [3] to find structural templates for docking which might be beyond the reach of sequence-based homology modeling approaches. In 2015, the Kpax program was extended to allow the flexible alignment and superposition of multiple protein structures, and a new multiple alignment quality measure has been developed. According to this quality measure, Kpax gives higher quality multiple structural alignments than all other published approaches. A journal article describing these new developments is under review.

• Contact: David Ritchie

• URL: http://kpax.loria.fr