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Integration of Molecular Dynamics Based Predictions into the Optimization of De Novo Protein Designs: Limitations and Benefits.
Computational Protein Design
Methods in molecular biology, January 2017
Henrique F. Carvalho, Arménio J. M. Barbosa, Ana C. A. Roque, Olga Iranzo, Ricardo J. F. Branco
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.
The data shown below were compiled from readership statistics for 22 Mendeley readers of this research output. Click here to see the associated Mendeley record.
|Readers by professional status||Count||As %|
|Student > Master||6||27%|
|Student > Bachelor||3||14%|
|Student > Ph. D. Student||3||14%|
|Readers by discipline||Count||As %|
|Agricultural and Biological Sciences||4||18%|
|Biochemistry, Genetics and Molecular Biology||3||14%|