The Amber biomolecular simulation programs

By David A. Case, Thomas E. Cheatham III, T. Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz Jr., Alexey V. Onufriev, Carlos Simmerling, Bing Wang, R. Woods. 2005

8,841 citations recorded by the source corpus.

Subfields: Cell Biology, Molecular Biology

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Citations in the corpus

A position-specific distance-dependent statistical potential for protein structure and functional study (2012, background): “, 1997; Sippl, 1990; Tanaka and Scheraga, 1976; Zhang and Zhang, 2010; Zhou and Zhou, 2002) compare favorably to physics-based potentials (Brooks et al., 2009; Bryngelson et al., 1995; Case et al., 2005; Dill, 1985, 1997; Dobson et al., 1998; Schuler et al., 2001; Shakhnovich, 2006) in many applicat”
Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer (2014, methodology): “For these systems, the best current software implementations of MD on commodity hardware or general-purpose supercomputers [6, 9, 21, 22, 36, 39] are limited to simulation rates of hundreds of nanoseconds of physical time per day of wall-clock time, even on the most powerful conventional…”
DOCK 6: combining techniques to model RNA-small molecule complexes. (2009, methodology): “AMBER Score implements molecular mechanics GB/SA simulations with the traditional all-atom AMBER force fields and the generalized AMBER force field (Wang et al. 2004; Case et al. 2005).”
Biological and synthetic membranes: What can be learned from a coarse-grained description? (2006, background): “de each column. In this case, the spectrum of the grid-averaged ﬂuctuations h(k) grid and the original spectrum, h(k) are related via |h(k) grid|2 = |h(k)|2 sin(∆kx/2) (∆kx/2) sin(∆ky/2) (∆kx/2) 2 (62) This discretization artifact becomes important when the ﬂuctuation spectrum of very small membran”
Fast and flexible design of novel proteins using graph neural networks (2019, methodology): “Using TLEAP in AMBER16 ( 47 ) and AMBER ff14SB force field ( 48 ), the structures were solvated by adding a 12 nm 3 box of explicit water molecules, TIP3P.”
The HDOCK server for integrated protein–protein docking (2020, methodology): “Then, the corresponding template-based complex of receptor and ligand can be constructed by superimposing the modeled receptor and ligand structures onto the complex template, where a 5,000-step AMBER MD minimization 66 is also conducted to remove severe atomic clashes at the interface.”
Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells (2007, methodology): “]. The AMBER99 force fields were used throughout these studies to optimize models. AMBER8 [”
Chemistry, structure and function of approved oligonucleotide therapeutics (2023, methodology): “The model was built with the program UCSF Chimera (265) and energyminimized with the Amber14 force field (266) (https:// ambermd.”
CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. (2018, methodology): “The CHARMM input, the glycolipid structure, as well as the topology and parameter files (for CHARMM, GROMACS, and AMBER) are downloadable in a single tar file (“download.tgz”).”