An overview of the Amber biomolecular simulation package

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High-accuracy refinement using Rosetta in CASP13 (2019, methodology): “…conformations close to this structure were structurally averaged to output a single refined model, which was subjected to restrained MD 7 using the AMBER suite 13 to improve modeling of explicit water molecule dependent structure features, followed by structural averaging and geometry optimization.”
Integrating protein structural dynamics and evolutionary analysis with Bio3D (2014, methodology): “org/Grantlab/bio3d) includes implementation of additional 3D visualization functionality, enhanced compatibility with the AMBER package [47], and further parallelization and optimization of structural alignment methods using graphical processing units (GPUs).”
The atomic simulation environment-a Python library for working with atoms. (2017, methodology): “For example, new interfaces to the ONETEP [152] and Amber [153] codes are currently being implemented.”
Using PyMOL as a platform for computational drug design (2017, methodology): “GTKDy-namo uses Amber 52 as a simulation engine in back-end.”
Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development (2020, methodology): “In another study, the binding modes of 2-anilinobenzamide derivatives in SIRT1/2/3 were investigated by 30-ns MD simulations with the AMBER 11.0 simulation package using the ff03.r1 [84] and ff99SB [14] force fields to explain the isoform selectivity of the compounds [89].”