Pairwise protein structure alignment

3D-Match implements pairwise protein structure alignment.
The algorithm implements a three-step procedure for aligning protein three-dimensional structures. The procedure includes building of the alignment core with the optimal RMSD, its expansion by introducing new protein fragments into the alignment, and optimization using dynamic programming to finally achieve an optimal alignment. 3D-Match aligns two polypeptide chains using C-alpha atomic coordinates, secondary structure characteristics are additionally used to weight the alignment.

Program is provided with viewer.

3D-Match description

3D-Match parameters