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Short Communication
A simple way to compute protein dynamics without a mechanical model
Article first published online: 13 APR 2007
DOI: 10.1002/prot.21430
Copyright © 2007 Wiley-Liss, Inc.
1097-0134/asset/cover.gif?v=1&s=d817e79b67ba6cacf8bdcce1a819c04de300a7e3 "Proteins: Structure, Function, and Bioinformatics")
Additional Information
How to Cite
Shih, C.-H., Huang, S.-W., Yen, S.-C., Lai, Y.-L., Yu, S.-H. and Hwang, J.-K. (2007), A simple way to compute protein dynamics without a mechanical model. Proteins: Structure, Function, and Bioinformatics, 68: 34–38. doi: 10.1002/prot.21430
Publication History
- Issue published online: 21 MAY 2007
- Article first published online: 13 APR 2007
- Manuscript Accepted: 16 JAN 2007
- Manuscript Received: 4 DEC 2006
Funded by
- National Science Council, Taiwan
- Abstract
- Article
- References
- Cited By
Keywords:
- protein dynamics;
- thermal fluctuations;
- molecular dynamics;
- normal mode analysis
Abstract
We found that in proteins the average atomic fluctuation is linearly related to the square of the atomic distance from the center of mass of the protein. Using this simple relation, we can accurately compute the temperature factors of proteins of a wide range of sizes and folds, and the correlation of the fluctuations in proteins. This simple relation provides a direct link between protein dynamics and the static protein's geometrical shape and offers a simple way to compute protein dynamics without either long time trajectory integration or any matrix operations. Proteins 2007. © 2007 Wiley-Liss, Inc.