Resultants and Loop Closure

By E. Coutsias, Chaok Seok, M. Wester, Ken A. Dill. 2006

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Accurate structure prediction of CDR H3 loops enabled by a novel structure-based C-terminal constraint (2016, background): “Similar to KIC, NGK generates diverse loop conformations by drawing w and c torsion angle pairs from Ramachandran distributions for all but three residues in the loop; the torsion angles of the remaining residues are determined analytically by polynomial resultants (41).”
Backbone flexibility in computational protein design. (2009, methodology): “This method was extended by techniques based on polynomial resultants [49] to enable sampling of interior torsions, bond angles, and bond lengths while solving the complete ensemble of values for the 6 closure torsions (Figure 1d).”
A computational method for the design of nested proteins by loop‐directed domain insertion (2018, background): “…decoy protein structures of each Insert Pair undergo iterative loop closure cycles of a generalized kinematic loop closure (KIC)-based algorithm, 36,42,43 which is a computationally inexpensive calculation that idealizes the peptide bonds at the four chain breakpoints (two at each end of each…”