Packing of sidechains in low-resolution models for proteins

Background: Atomic level rotamer libraries for sidechains in proteins have been proposed by several groups. Conformations of side groups in coarse-grained models, on the other hand, have not yet been analyzed, although low resolution approaches are the only efficient way to explore global structural features. Results: A residue-specific backbone-dependent library for sidechain isomers, compatible with a coarse-grained model, is proposed. The isomeric states are utilized in packing sidechains of known backbone structures. Sidechain positions are predicted with a root-mean-square deviation (rmsd) of 2.40 Angstrom with respect to crystal structure for 50 test proteins. The rmsd for core residues is 1.60 Angstrom and decreases to 1.35 Angstrom when conformational correlations and directional effects in inter-residue couplings are considered. Conclusions: An automated method for assigning sidechain positions in coarse-grained model proteins is proposed and made available on the internet; the method accounts satisfactorily for sidechain packing, particularly in the core.