In-silico mutagenesis
To assess the consistency of the predicted CENP-HIKM organizational pattern with experimental reports from previous studies [14, 37],in-silico mutants of the CENP-H and CENP-M were designed using the Chimera-curated backbone-dependent Dunbrack rotamer library [42]. The backbone-dependent rotamer library is composed of variances, rotamer frequencies, and mean dihedral angles as a function of the backbone dihedral angles. The prediction of structures and methods of design that utilizes backbone flexibility benefit strongly from smoothly varying angles and probabilities. A new backbone-dependent rotamer library version was developed to use adaptive kernel regression for variances and mean dihedral angle calculations and also the adaptive kernel density calculations for the frequency of rotamers. This design creates an avenue for the estimation of variances, probabilities of rotamers, and mean angles as a continuous and smooth function of psi and phi [42]. The estimation of continuous probability density for the nonrotameric degrees of freedom of aromatic side chains, amides, and carboxylates was modeled as a function of the rotamers and backbone dihedrals of the residual degrees of freedom.