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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.