Paper Citing NAMD - Abstract
Anitescu, Mihai; Park, Sanghyun
A linear assignment approach for the least-squares protein morphing problem
MATHEMATICAL PROGRAMMING, 125:195-203, SEP 2010
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 sigma 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.
