Figure 4

Monte Carlo side chain optimization of barnase-barstar complex using Hunter. A model of the complex (PDB ID 1BRS) with the lowest score has a side chain RMSD of 1.44 Å (filled triangle; gray dots in the plot are the conformations sampled during a MCSA run). The native structure (filled circle) is never attainable in the side chain modelling due to use of a discrete rotamer library. Instead, the best rotameric structure for the complex would have a RMSD of 0.43 Å (filled square). None of the conformations in the region between 0.43 Å and 1.44 Å is ever sampled. To investigate this problem, a MCSA run was started from the best-rotameric structure (see inset). As can be seen in the inset, such a MCSA run, nevertheless, converges to the same region as a standard run.