Assessment of rotamer library for protein structure prediction

Side chain packing is a crucial step for protein structure prediction. And the quality of rotamer library has important implications in side chain packing. This paper assess dunbrack rotamer libraries and simple sampling rotamer libraries for certain structures by comparing the native structure and solutions come from rotamer libraries. Results of eleven hard targets in CASP9 show that the best solution is near to the native structure. Otherwise, there is no native structure in protein structure prediction.We compare the best solutions which choosing by lower RMSD and energy, it shows that the best solution which choosing by lower energy is near to the best solution which choosing by low RMSD. So, in the case of unknown native structure, the energy guided choosing is necessary, but it must adopt some other method such as clustering to select the best solution.