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The Amber biomolecular simulation programs
Journal article   Open access  Peer reviewed

The Amber biomolecular simulation programs

David A Case, Thomas E Cheatham, 3rd, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M Merz, Jr, Alexey Onufriev, Carlos Simmerling, Bing Wang and Robert J Woods
Journal of computational chemistry, Vol.26(16), pp.1668-1688
12/2005
PMCID: PMC1989667
PMID: 16200636

Abstract

Algorithms Carbohydrates - chemistry Computer Simulation - trends Models, Biological Models, Chemical Models, Molecular Nucleic Acids - chemistry Proteins - chemistry Software - trends Thermodynamics
We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
url
https://doi.org/10.1002/jcc.20290View
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