Molecular dynamics: survey of methods for simulating the activity of proteins.

By Stewart A. Adcock, James Andrew McCammon. Chemical Reviews, 2006

1,196 citations recorded by the source corpus.

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

View Paper: https://www.semanticscholar.org/paper/8d3353f6802053ea9edb5c76d099aba99eec884f

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In Atomic and Molecular Physics, and Optics

In Molecular Biology

Citations in the corpus

Anton, a special-purpose machine for molecular dynamics simulation (2008, methodology): “mD comPutation on anton An MD computation simulates the motion of a collection of atoms (the chemical system) over a period of time according to the laws of classical physics.(1) Time is broken into a series of discrete time steps, each representing a few femtoseconds of simulated time.”
Dynamic personalities of proteins (2007, background): “Impressive progress has been made in the development of these force fields since their original conceptio”
Computational modeling of phosphotransfer complexes in two-component signaling. (2010, background): “Typically, one has to balance the accuracy of description/physics with the available computational resources (Adcock and McCammon, 2006).”
Discovery Through the Computational Microscope (2009, positive): “structural data into the dynamic domain (Karplus and Petsko, 1990; Daggett and Levitt, 1993; Adcock and McCammon, 2006; Sotomayor and Schulten, 2007).”
Molecular dynamics simulations and drug discovery (2011, background): “These techniques, which include thermodynamic integration [54], single-step perturbation [55], and free energy perturbation [56], are based in large part on molecular dynamics simulations.”
Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview (2018, background): “…of atoms along time by the integration of Newton’s equations of motions (classical mechanics), reported in the following equation (Leach, 2001; Adcock and McCammon, 2006). with F i (t) force exerted on atom i at time t , r i (t) vector position of the atom i at time t , m i mass of the atom (…”