Summary: APPENDIX A: SUPPLEMENTARY MATERIAL
As we see in Fig. 2, the hub of the algorithm is the M matrix. Matrix element Mi
j
represents the best way to fold the prefixes s[1..i] and t[1..j] given that i and j are paired.
Mi
j = min Mi-1
j-1 + NN(i, j), (A1a)
tstack(i - 1, j - 1) + Ginit + GAU/GU (i, j), (A1b)
Mi-2
j-1 + NN (i, j, i - 2, j - 1) + Gbulge, (A1c)
Mi-1
j-2 + NN (i, j, i - 1, j - 2) + Gbulge, (A1d)
Mi-2
j-2 + il1x1(i, j), Mi-2
j-3 + il1x2(i, j), (A1e)
Mi-3
j-2 + il2x1(i, j), Mi-3
j-3 + il2x2(i, j), (A1f)
Bi-1
j-1 + GAU/GU (i, j), bi-1

Source: Aalberts, Daniel P. - Department of Physics, Williams College

Collections: Physics