Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.

By D. Hamelberg, John T Mongan, James Andrew McCammon. Journal of Chemical Physics, 2004

1,418 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0d743061cbb5d454947fb76d5a11f39e754f9175

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In Atomic and Molecular Physics, and Optics

In Molecular Biology

Citations in the corpus

Dynamic personalities of proteins (2007, methodology): “Alternatively, the dynamic process is accelerated by external force to access this timescale (used in methods such as targeted, steered and accelerated molecular-dynamics simulation”
Computer-aided drug-discovery techniques that account for receptor flexibility. (2010, positive): “These so-called accelerated molecular dynamics simulations address concerns about inadequate conformational sampling and may prove useful in future drug-design efforts [37,38].”
Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview (2018, background): “V min will allow maintaining the underlying shape of the landscape (Hamelberg et al., 2004).”
The future of molecular dynamics simulations in drug discovery (2011, background): “Several distinct, atomistic approaches aim to accelerate the still-insufﬁcient sampling of protein conformational states, for example metadynamics [48], accelerated MD [49], and temperature accelerated MD [50].”
Molecular dynamics simulations and drug discovery (2011, background): “For example, in accelerated molecular dynamics (aMD) [32,33], large energy barriers are artificially reduced.”
Weighted Ensemble Simulation: Review of Methodology, Applications, and Software (2017, neutral): “Thus, in contrast to other approaches for accessing long-timescale motions such as metadynamics (43), accelerated MD (34), and replica exchange (35, 47), path sampling approaches enable rigorous, straightforward calculations of rate constants without additional assumptions.”
An overview of the Amber biomolecular simulation package (2013, background): “Accelerated molecular dynamics (AMD) 24 , 25 adds a bias to the potential function that can facilitate crossing of high energy barriers without advance knowledge of the location of either the potential energy wells or saddle points.”