Abstract
Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis.
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Acknowledgments
The authors thank the financial support from Fundação para a Ciência e a Tecnologia, Portugal, through contracts SFRH/BD/90644/2012 (H.F.C.), SFRH/BPD/69163/2010 (R.J.F.B.), and ERA-IB-2/0001/2013. This work was supported by the Unidade de Ciõncias Biomoleculares Aplicadas-UCIBIO, which is financed by national funds from FCT/MEC (UID/Multi/04378/2013) and co-financed by the ERDF under the PT2020 Partnership Agreement (POCI-01-0145-FEDER-007728). The authors would like to thank also the support from Centre National de la Recherche Scientifique (CNRS), France and FCT, Portugal, through the International Program of Scientific Cooperation (PROJECT PICS-147340).
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Carvalho, H.F., Barbosa, A.J.M., Roque, A.C.A., Iranzo, O., Branco, R.J.F. (2017). Integration of Molecular Dynamics Based Predictions into the Optimization of De Novo Protein Designs: Limitations and Benefits. In: Samish, I. (eds) Computational Protein Design. Methods in Molecular Biology, vol 1529. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6637-0_8
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DOI: https://doi.org/10.1007/978-1-4939-6637-0_8
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Online ISBN: 978-1-4939-6637-0
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