Computing conformational free energy by deactivated morphing

Sanghyun Park; Albert Y. Lau; Benòt Roux

doi:10.1063/1.2982170

Computing conformational free energy by deactivated morphing

Sanghyun Park, Albert Y. Lau, Benòt Roux

Research output: Contribution to journal › Article › peer-review

22 Scopus citations

Abstract

Despite the significant advances in free-energy computations for biomolecules, there exists no general method to evaluate the free-energy difference between two conformations of a macromolecule that differ significantly from each other. A crucial ingredient of such a method is the ability to find a path between different conformations that allows an efficient computation of the free energy. In this paper, we introduce a method called "deactivated morphing," in which one conformation is morphed into another after the internal interactions are completely turned off. An important feature of this method is the (shameless) use of nonphysical paths, which makes the method robustly applicable to conformational changes of arbitrary complexity.

Original language	English (US)
Article number	134102
Journal	Journal of Chemical Physics
Volume	129
Issue number	13
DOIs	https://doi.org/10.1063/1.2982170
State	Published - 2008
Externally published	Yes

ASJC Scopus subject areas

General Physics and Astronomy
Physical and Theoretical Chemistry

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10.1063/1.2982170

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abstract = "Despite the significant advances in free-energy computations for biomolecules, there exists no general method to evaluate the free-energy difference between two conformations of a macromolecule that differ significantly from each other. A crucial ingredient of such a method is the ability to find a path between different conformations that allows an efficient computation of the free energy. In this paper, we introduce a method called {"}deactivated morphing,{"} in which one conformation is morphed into another after the internal interactions are completely turned off. An important feature of this method is the (shameless) use of nonphysical paths, which makes the method robustly applicable to conformational changes of arbitrary complexity.",

author = "Sanghyun Park and Lau, {Albert Y.} and Ben{\`o}t Roux",

note = "Funding Information: S.P. thanks Vijay Pande for guidance during the early stages of the work and Chris Jarzynski for stimulating discussions on rotational entropy. This research was supported by the U.S. Department of Energy under Contract No. DE-AC02-06CH11357.",

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AU - Roux, Benòt

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AB - Despite the significant advances in free-energy computations for biomolecules, there exists no general method to evaluate the free-energy difference between two conformations of a macromolecule that differ significantly from each other. A crucial ingredient of such a method is the ability to find a path between different conformations that allows an efficient computation of the free energy. In this paper, we introduce a method called "deactivated morphing," in which one conformation is morphed into another after the internal interactions are completely turned off. An important feature of this method is the (shameless) use of nonphysical paths, which makes the method robustly applicable to conformational changes of arbitrary complexity.

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Computing conformational free energy by deactivated morphing

Abstract

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