Abstract
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.
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Acknowledgments
This work was supported by grants from CNPq (Brazil) (308883/2014-4). This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior—Brasil (CAPES)—Finance Code 001. GB-F acknowledges support from PUCRS/BPA fellowship. WFA is a senior researcher for CNPq (Brazil) (Process Numbers: 308883/2014-4 and 309029/2018-0).
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Bitencourt-Ferreira, G., de Azevedo, W.F. (2019). Molecular Dynamics Simulations with NAMD2. In: de Azevedo Jr., W. (eds) Docking Screens for Drug Discovery. Methods in Molecular Biology, vol 2053. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9752-7_8
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