The TreePack program uses a tree-decomposition based algorithm to solve the side-chain packing problem more efficiently. This algorithm is more efficient than SCWRL 3.0 while maintaining the same level of accuracy.
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Jinbo Xu and Bonnie Berger.
Fast and accurate algorithms for protein side-chain packing.
The Journal of the ACM, Volume 53, Issue 4 (July 2006), pp. 533-557.