Background: Atomic level rotamer libraries for sidechains in proteins have
been proposed by several groups. Conformations of side groups in coarse-gra
ined models, on the other hand, have not yet been analyzed, although low re
solution approaches are the only efficient way to explore global structural
features.
Results: A residue-specific backbone-dependent library for sidechain isomer
s, 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 A
ngstrom with respect to crystal structure for 50 test proteins. The rmsd fo
r core residues is 1.60 Angstrom and decreases to 1.35 Angstrom when confor
mational correlations and directional effects in inter-residue couplings ar
e considered.
Conclusions: An automated method for assigning sidechain positions in coars
e-grained model proteins is proposed and made available on the internet; th
e method accounts satisfactorily for sidechain packing, particularly in the
core.