The Amber biomolecular simulation programs

被引：7761

作者：

Case, DA

Cheatham, TE

Darden, T

Gohlke, H

Luo, R

Merz, KM

Onufriev, A

Simmerling, C

Wang, B

Woods, RJ

机构：

[1] Scripps Res Inst, Dept Mol Biol, La Jolla, CA 92037 USA

[2] Univ Utah, Dept Med Chem, Salt Lake City, UT 84112 USA

[3] Univ Utah, Dept Pharmaceut & Pharmaceut Chem, Salt Lake City, UT 84112 USA

[4] Univ Utah, Dept Bioengn, Salt Lake City, UT 84112 USA

[5] NIEHS, Struct Biol Lab, Res Triangle Pk, NC 27709 USA

[6] Goethe Univ Frankfurt, Fachbereich Biol & Informat, D-60439 Frankfurt, Germany

[7] Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92697 USA

[8] Penn State Univ, Dept Chem, University Pk, PA 16802 USA

[9] Virginia Tech, Dept Comp Sci, Blacksburg, VA 24061 USA

[10] SUNY Stony Brook, Dept Chem, Stony Brook, NY 11794 USA

[11] Univ Georgia, Complex Carbohydrate Res Ctr, Athens, GA 30602 USA

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2005年 / 26卷 / 16期

关键词：

Amber; biomolecular simulation programs;

D O I：

10.1002/jcc.20290

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

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. (c) 2005 Wiley Periodicals, Inc.

引用

页码：1668 / 1688

页数：21

共 149 条

[91] Exploring protein native states and large-scale conformational changes with a modified generalized born model [J].