Molecular dynamics and protein function
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Open Access
- 3 May 2005
- journal article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 102 (19) , 6679-6685
- https://doi.org/10.1073/pnas.0408930102
Abstract
A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled with improvements in methodology makes this an exciting time for the application of simulation to structural biology. In this Perspective we survey two areas, protein folding and enzymatic catalysis, in which simulations have contributed to a general understanding of mechanism. We also describe results for the F1ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems.Keywords
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