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

Input:

sequences P = (p₁,…,p _n ), Q = (q₁,…,q _m ) and $\ell \in \mathbb{I}$.

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) |P^′| = ℓ,

(B) d = RMSD(P^′,f(p^′)) is minimized.