Torsion angle flexibility

Based on the RIS Ansatz, the embedding algorithm benefits from a great flexibility in the choice of the input parameters that account for the local chain energy configuration the input for the correlations of torsion angles along the chain backbones can be either calculated with the help of a force field, or extracted from measurements, or even biased in order to study any thinkable structural properties of the macromolecules. 

Several remedies have been suggested for improving the PB based pKa prediction methods. Most of them are based on strategies that combine conformational flexibility with the PB calculation. You and Bashford included multiple conformers by systematically scanning the side chain torsion angles [107], Alexov and Gunner used Monte-Carlo protocol to sample positions of hydroxyl and other polar protons [1], This method, referred to as the multi-conformation continuum electrostatic (MCCE), was later extended to include rotamers for residues that have strong electrostatic... 

While most CA s of disaccharides have depended only on intrinsic characteristics of the molecule, experimental results depend strongly on the environment. By experiment, Kamide and Saito ( ) have shown that the degree of flexibility of cellulose and its derivatives is strongly dependent on the dielectric constant of the solvent as well as the exact type and degree of substitution. Since a substantial portion of the polymer flexibility depends on the extent of variability of the torsion angles at the intermonomer linkage, the dependence of polymer flexibility on type of solvent and substitution means that the disaccharide flexibility also should depend on those factors. Non-polar solvents allowed the molecules to have greater flexibility than did polar solvents (35). 

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