The Amber biomolecular simulation programs
David A. CaseDepartment of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, CA 92037, USA. [email protected]Thomas E. CheathamDepartments of Medicinal Chemistry, Pharmaceutics & Pharmaceutical Chemistry, and Bioengineering, 2000 East, 30 South, Skaggs Hall 201, University of Utah, Salt Lake City, Utah 84112Tom DardenNational Institute of Environmental Health Sciences, Laboratory of Structural Biology, Mail Drop F3-02, PO Box 12233 Research Triangle Park, North Carolina 27709Holger GohlkeFachbereich Biologie und Informatik, J.W. Goethe-Universität, Marie-Curie-Str. 9, 60439 Frankfurt/Main, GermanyRay LuoDepartment of Molecular Biology and Biochemistry, University of California, 5.3206 Natural Science I, Irvine, California 92697Kenneth M. MerzDepartment of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802Alexey V. OnufrievDepartment of Computer Science, Virgina Tech, 600 McBryde (MC 0106) Blacksburg, Virginia 24061Carlos SimmerlingDepartment of Chemistry, Stony Brook University, Stony Brook, New York 11794Bing WangDepartment of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, California 92037Robert J. WoodsComplex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, Georgia 30602
2005en
ABI
Аннотация
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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