A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions

摘要

Rotamer libraries are used in protein structure determination, structure prediction, and design. The backbone-dependent rotamer library consists of rotamer frequencies and their mean dihedral angles and variances as a function of the backbone dihedral angles ϕ and ψ. Previous versions of this rotamer library were not developed with smoothness in mind, although some structure prediction and protein design methods would strongly benefit from smoothing. A new version of the backbone-dependent rotamer library has been developed using adaptive kernel density estimates for the rotamer frequencies and adaptive kernel regression for the mean dihedral angles and variances. The formulation presented allows for evaluation of the rotamer probabilities, mean angles and variances at any ϕ, ψ point, i.e. as a continuous function of ϕ and ψ. Continuous probability density estimates for the non-rotameric degrees of freedom of amides, carboxylates, and aromatic side chains have been modeled as a function of the backbone dihedral angles and rotamers of the remaining degrees of freedom. New backbone-dependent rotamer libraries at varying levels of smoothing are available from .