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Table 1 Largest Common Point (LCP) set problem definition under RMSD

From: The difficulty of protein structure alignment under the RMSD

 

LCP problem by the RMSD measure

Input:

sequences P = (p1,…,p n ), Q = (q1,…,q m ) and distance

 

threshold θR. Without loss of generality assume m ≥ n.

Output:

(i) subsequences PP, QQ, |P| = |Q|, and

 

(ii) bijection f:PQ, fulfilling the following conditions:

 

(A) RMSD(P,f(P)) ≤ θ,

 

(B) the score l = |P| is maximized.