The Amber biomolecular simulation programs

  1. David A. Case1,*,
  2. Thomas E. Cheatham III2,
  3. Tom Darden3,
  4. Holger Gohlke4,
  5. Ray Luo5,
  6. Kenneth M. Merz Jr.6,
  7. Alexey Onufriev7,
  8. Carlos Simmerling8,
  9. Bing Wang1,
  10. Robert J. Woods9

Article first published online: 30 SEP 2005

DOI: 10.1002/jcc.20290

Issue

Journal of Computational Chemistry

Journal of Computational Chemistry

Volume 26, Issue 16, pages 1668–1688, December 2005

Additional Information

How to Cite

Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B. and Woods, R. J. (2005), The Amber biomolecular simulation programs. J. Comput. Chem., 26: 1668–1688. doi: 10.1002/jcc.20290

Author Information

  1. 1

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, California 92037

  2. 2

    Departments of Medicinal Chemistry, Pharmaceutics & Pharmaceutical Chemistry, and Bioengineering, 2000 East, 30 South, Skaggs Hall 201, University of Utah, Salt Lake City, Utah 84112

  3. 3

    National Institute of Environmental Health Sciences, Laboratory of Structural Biology, Mail Drop F3-02, PO Box 12233 Research Triangle Park, North Carolina 27709

  4. 4

    Fachbereich Biologie und Informatik, J.W. Goethe-Universität, Marie-Curie-Str. 9, 60439 Frankfurt/Main, Germany

  5. 5

    Department of Molecular Biology and Biochemistry, University of California, 5.3206 Natural Science I, Irvine, California 92697

  6. 6

    Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802

  7. 7

    Department of Computer Science, Virgina Tech, 600 McBryde (MC 0106) Blacksburg, Virginia 24061

  8. 8

    Department of Chemistry, Stony Brook University, Stony Brook, New York 11794

  9. 9

    Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, Georgia 30602

*Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, California 92037

Publication History

  1. Issue published online: 30 SEP 2005
  2. Article first published online: 30 SEP 2005
  3. Manuscript Accepted: 5 MAR 2005
  4. Manuscript Received: 7 JAN 2005

Funded by

  • NIH. Grant Number: RR12255

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Keywords:

  • Amber;
  • biomolecular simulation programs

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. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1668–1688, 2005

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