Constructing side chains on near-native main chains for ab initio protein structure prediction

Is there value in constructing side chains while searching protein conforma tional space during an ab initio simulation? If so, what is the most comput ationally efficient method for constructing these side chains? To answer th ese questions, four published approaches were used to construct side chain conformations on a range of near-native main chains generated by ab initio protein structure prediction methods. The accuracy of these approaches was compared with a naive approach that selects the most frequently observed ro tamer for a given amino acid to construct side chains. An all-atom conditio nal probability discriminatory function is useful at selecting conformation s with overall low all-atom root mean square deviation (r.m.s.d.) and the d iscrimination improves on sets that are closer to the native conformation. In addition, the naive approach performs as well as more sophisticated meth ods in terms of the percentage of chi(1) angles built accurately and the al l-atom r.m.s.d., between the native and near-native conformations. The resu lts suggest that the naive method would be extremely useful for fast and ef ficient side chain construction on vast numbers of conformations for ab ini tio prediction of protein structure.