The Amber biomolecular simulation programs

David A. Case; Thomas E. Cheatham; Tom Darden; Holger Gohlke; Ray Luo; Kenneth M. Merz; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J. Woods

doi:10.1002/jcc.20290

The Amber biomolecular simulation programs

David A. Case
, Thomas E. Cheatham
, Tom Darden
, Holger Gohlke
, Ray Luo
, Kenneth M. Merz
, Alexey Onufriev
, Carlos Simmerling
, Bing Wang
, Robert J. Woods

Laufer Center for Physical and Quantitative Biology

Scripps Research Institute
University of Utah
National Institutes of Health
Goethe University Frankfurt
University of California at Irvine
Pennsylvania State University
Virginia Polytechnic Institute and State University
University of Georgia

Research output: Contribution to journal › Review article › peer-review

8484 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	1668-1688
Number of pages	21
Journal	Journal of Computational Chemistry
Volume	26
Issue number	16
DOIs	https://doi.org/10.1002/jcc.20290
State	Published - Dec 2005

Keywords

Amber
Biomolecular simulation programs

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10.1002/jcc.20290

Cite this

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abstract = "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.",

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AU - Onufriev, Alexey

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AU - Wang, Bing

AU - Woods, Robert J.

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AB - 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.

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The Amber biomolecular simulation programs

Abstract

Keywords

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