X-ray diffraction crystallography is the primary technique to determine the three-dimensional structures of biomolecules. Although a robust method, X-ray crystallography is not able to access the dynamical behavior of macromolecules. To do so, we have to carry out molecular dynamics simulations taking as an initial system the three-dimensional structure obtained from experimental techniques or generated using homology modeling. In this chapter, we describe in detail a tutorial to carry out molecular dynamics simulations using the program NAMD2. We chose as a molecular system to simulate the structure of human cyclin-dependent kinase 2.
CITATION STYLE
Bitencourt-Ferreira, G., & de Azevedo, W. F. (2019). Molecular dynamics simulations with NAMD2. In Methods in Molecular Biology (Vol. 2053, pp. 109–124). Humana Press Inc. https://doi.org/10.1007/978-1-4939-9752-7_8
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