Table 1 Algorithm MAPSCI: Multiple Alignment of Protein Structures and Consensus Identification

2. Do

3.    if i = 0 then compute pairwise structure alignment between and every P _j .

4.    else use standard dynamic programming to align with every P _j .

5.    i ← i + 1.

6.    Compute correspondence from the above alignments (either pairwise or dynamic programming) using center-star-like method.

7.    Compute optimal translation matrix and optimal rotation matrix iteratively (Theorems 2 and 3). Transform P _j by and for every j to obtain multiple structure alignment ℳⁱ. SCⁱ← SC(ℳⁱ).

8. Post-process ℳⁱby removing all columns consisting of only gaps.

9.    Compute new consensus structure from ℳⁱby Theorem 1.

10. Until .//η is a user-specified threshold (currently set at 0.0001)