A simple alternating method - from superposition to alignment
From Superposition to scoring matrix and alignment
- let d(Ai,Bj) be the Euclidean distance between Ai and Bj after superposition
- let ? be the upper limit on distance between residues to be rewarded
- R is a scoring matrix that can be used for DP alignment of the superposed structures
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- zero gap penalty, and allow zero diagonal step