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. 2010 Jul 12;11:374. doi: 10.1186/1471-2105-11-374

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Copyright ©2010 Potapov et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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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.