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 first backbone-dependent rotamer library was developed in 1993 by Roland Dunbrack and Martin Karplus to assist the prediction of the Cartesian coordinates of a protein's side chains given the experimentally determined or predicted Cartesian coordinates of its main chain. The library was derived from the structures of 132 proteins from the Protein Data Bank with resolution of 2.0 Å or better. 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. The Bayesian approach provided the opportunity for the definition of a Bayesian prior for the frequencies of rotamers in each 10° x 10° bin derived by assuming that the steric and electrostatic effects of the φ and ψ dihedral angles are independent. In addition, a periodic kernel with 180° periodicity was used to count side chains 180° away in each direction from the bin of interest.