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Table 2 Minimum Aligned Distance (MAD) problem definition under RMSD

From: The difficulty of protein structure alignment under the RMSD

  MAD problem by the RMSD measure
Input: sequences P = (p1,…,p n ), Q = (q1,…,q m ) and I.
  Without loss of generality assume m ≥ n.
Output: (i) subsequences PP, QQ, |P| = |Q|, and
  (ii) bijection f:PQ, fulfilling the following conditions:
  (A) |P| = ,
  (B) d = RMSD(P,f(p)) is minimized.