A linear assignment approach for the least-squares protein morphing problem |
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Authors: | Mihai Anitescu Sanghyun Park |
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Institution: | 1. Mathematics and Computer Science Division, Building 221, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
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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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