A linear assignment approach for the least-squares protein morphing problem

• 成果类型: Article
• 署名作者: Anitescu, Mihai; Park, Sanghyun
• 署名单位: United States Department of Energy (DOE); Argonne National Laboratory
• 刊物名称: MATHEMATICAL PROGRAMMING
• ISSN/ISSBN: 0025-5610
• DOI: 10.1007/s10107-009-0269-6
• 发表日期: 2010
• 页码: 195-203
• 关键词: molecular-dynamics

摘要

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.