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Abstract:
Abstract
Brownian dynamics (BD) is a computational method to simulate molecular diffusion processes. Although the BD method has been developed over several decades and is well established, new methodological developments are improving its accuracy, widening its scope, and increasing its application. In biological applications, BD is used to investigate the diffusive behavior of molecules subject to forces due to intermolecular interactions or interactions with material surfaces. BD can be used to compute rate constants for diffusional association, generate structures of encounter complexes for molecular binding partners, and examine the transport properties of geometrically complex molecules. Often, a series of simulations is performed, for example, for different protein mutants or environmental conditions, so that the effects of the changes on diffusional properties can be estimated. While biomolecules are commonly described at atomic resolution and internal molecular motions are typically neglected, coarse‐graining and the treatment of conformational flexibility are increasingly employed. Software packages for BD simulations of biomolecules are growing in capabilities, with several new packages providing novel features that expand the range of questions that can be addressed. These advances, when used in concert with experiment or other simulation methods, such as molecular dynamics, open new opportunities for application to biochemical and biological systems. Here, we review some of the latest developments in the theory, methods, software, and applications of BD simulations to study biomolecular diffusional association processes and provide a perspective on their future use and application to outstanding challenges in biology, bioengineering, and biomedicine.
This article is categorized under:
Structure and Mechanism > Computational Biochemistry and Biophysics
Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods
Software > Simulation Methods
SEEK ID: https://publications.h-its.org/publications/1555
DOI: 10.1002/wcms.1649
Research Groups: Molecular and Cellular Modeling
Publication type: Journal
Journal: WIREs Computational Molecular Science
Citation: WIREs Comput Mol Sci 13(3),e1649
Date Published: 1st May 2023
Registered Mode: by DOI
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Citation
Muñiz‐Chicharro, A., Votapka, L. W., Amaro, R. E., & Wade, R. C. (2022). Brownian dynamics simulations of biomolecular diffusional association processes. In WIREs Computational Molecular Science (Vol. 13, Issue 3). Wiley. https://doi.org/10.1002/wcms.1649
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Created: 16th Dec 2022 at 12:24
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