From: The difficulty of protein structure alignment under the RMSD
LCP problem by the RMSD measure | |
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Input: | sequences P = (p1,…,p n ), Q = (q1,…,q m ) and distance |
threshold . Without loss of generality assume m ≥ n. | |
Output: | (i) subsequences P′ ⊆ P, Q′ ⊆ Q, |P′| = |Q′|, and |
(ii) bijection f:P′ ↦ Q′, fulfilling the following conditions: | |
(A) RMSD(P′,f(P′)) ≤ θ, | |
(B) the score l = |P′| is maximized. |