Abstract
This work addresses the computation of free-energy differences between protein conformations by using morphing (i.e., transformation) of a source conformation into a target conformation. To enhance the morphing procedure, we employ permutations of atoms: we seek to find the permutation σ that minimizes the mean-square distance traveled by the atoms. Instead of performing this combinatorial search in the space of permutations, we show that the best permutation can be found by solving a linear assignment problem. We demonstrate that the use of such optimal permutations significantly improves the efficiency of the free-energy computation.
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Anitescu, M., Park, S. A linear assignment approach for the least-squares protein morphing problem. Math. Program. 125, 195–203 (2010). https://doi.org/10.1007/s10107-009-0269-6
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DOI: https://doi.org/10.1007/s10107-009-0269-6