The Inapproximability of Side-Chain Positioning

Side-chain positioning is a central component of homology modeling and protein design. In a common formulation of the problem, the backbone is fixed, side-chain conformations come from a rotamer library, and a pairwise energy function is optimized. In [5], we showed that it is NP-complete to find even a reasonable approximate solution to this problem. Here, we explain, for non-computer scientists, the result in more detail.

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