Backbone-dependent rotamer library

In biochemistry, a backbone-dependent rotamer library provides the frequencies, mean dihedral angles, and standard deviations of the discrete conformations (known as rotamers) of the amino acid side chains in proteins as a function of the backbone dihedral angles φ and ψ of the Ramachandran map.

By contrast, backbone-independent rotamer libraries express the frequencies and mean dihedral angles for all side chains in proteins, regardless of the backbone conformation of each residue type.

Backbone-dependent rotamer libraries have been shown to have significant advantages over backbone-independent rotamer libraries, principally when used as an energy term, by speeding up search times of side-chain packing algorithms used in protein structure prediction and protein design.

The library provided the counts and frequencies of χ1 or χ1+χ2 rotamers of 18 amino acids (excluding glycine and alanine residue types, since they do not have a χ1 dihedral) for each 20° x 20° bin of the Ramachandran map (φ,ψ = -180° to -160°, -160° to -140° etc.).

In 1997, Dunbrack and Fred E. Cohen at the University of California, San Francisco presented a backbone-dependent rotamer library derived from Bayesian statistics.

When ψ is -60° and χ1 is +60° (the g+ rotamer of a side chain), there is a steric interaction between N(i+1) and Cγ because the dihedral angles connecting them are N(i+1)-C(i)-Cα(i)-Cβ(i) = ψ+120° = +60°, and C(i)-Cα(i)-Cβ(i)-Cγ(i) = χ1-120° = -60°.

The Dunbrack backbone-dependent rotamer library is used in a number of programs for protein structure prediction and computational design, including: