Brownian dynamics
Introduction
Brownian dynamics is a methods that allows the diffusional motions of solutes to be simulated in implicit solvent.
In Brownian dynamics (BD) simulations, solute particles diffuse in a solvent that is modelled as a continuum that influences interparticle forces, and exerts stochastic and frictional effects on particle motion. BD simulations provide a powerful tool to study biomolecular recognition processes accounting for hydrodynamic interactions. They can, for example, be used to compute bimolecular association rate constants, to dock molecules to predict the structure of their complex, and to investigate the effects of macromolecular crowding on molecular association processes.
Example Cases
For examples of previously performed studies in which Brownian dynamics was the primary method used, see the following example cases:
- Molecular Mechanics Study of Flow and Surface Influence in Ligand-Protein Association.
- Multiscale Approach for Computing Gated Ligand Binding from Molecular Dynamics and Brownian Dynamics Simulations.
- Multiscale Simulations Examining Glycan Shield Effects on Drug Binding to Influenza Neuraminidase.
- Receptor-Ligand Rebinding Kinetics in Confinement.
- Role of secondary sialic acid binding sites in influenza N1 neuraminidase.
- Protein-protein association: investigation of factors influencing association rates by brownian dynamics simulations.
- Brownian dynamics simulation of protein-protein diffusional encounter.
- Simulation of the diffusional association of barnase and barstar.
Brownian dynamics was also used in the following examples:
- Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach.
- Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach.
- SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.
- Multiscale Simulation of Receptor-Drug Association Kinetics: Application to Neuraminidase Inhibitors.
- Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.
Tutorials
The folowing tutorial describes the use of Brownian dynamics: