Fig. 4From: MADOKA: an ultra-fast approach for large-scale protein structure similarity searchingSchematic diagram of MADOKA algorithm and the web interface. The algorithm involves two steps: 1) Search for Longest-Common-Subsequence (LCS) for each pairwise secondary structure elements using dynamic programming, and then structure pairs with the length of the LCS below the threshold are removed; 2) Pairwise 3D residue structural rigid body superposition is performed and residue-level alignments are constructed, and the best alignment with the highest TM-score and optimally aligned position for each pair of protein structures is selectedBack to article page