Integration of molecular dynamics based predictions into the optimization of de novo protein designs: Limitations and benefits

Henrique F Carvalho, Arménio J M Barbosa, Ana C A Roque, Olga Iranzo, Ricardo J F Branco

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

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.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc
Pages181-201
Number of pages21
Volume1529
DOIs
Publication statusPublished - 2017

Publication series

NameMethods in Molecular Biology
Volume1529
ISSN (Print)10643745

Fingerprint

Molecular Dynamics Simulation
Proteins
Software

Keywords

  • Elastic network models
  • Internal molecular dynamics
  • Normal mode analysis
  • Principal component analysis
  • Protein essential dynamics

Cite this

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 Methods in Molecular Biology (Vol. 1529, pp. 181-201). (Methods in Molecular Biology; Vol. 1529). Humana Press Inc. https://doi.org/10.1007/978-1-4939-6637-0_8
Carvalho, Henrique F ; Barbosa, Arménio J M ; Roque, Ana C A ; Iranzo, Olga ; Branco, Ricardo J F. / Integration of molecular dynamics based predictions into the optimization of de novo protein designs : Limitations and benefits. Methods in Molecular Biology. Vol. 1529 Humana Press Inc, 2017. pp. 181-201 (Methods in Molecular Biology).
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Carvalho, HF, Barbosa, AJM, Roque, ACA, Iranzo, O & Branco, RJF 2017, Integration of molecular dynamics based predictions into the optimization of de novo protein designs: Limitations and benefits. in Methods in Molecular Biology. vol. 1529, Methods in Molecular Biology, vol. 1529, Humana Press Inc, pp. 181-201. https://doi.org/10.1007/978-1-4939-6637-0_8

Integration of molecular dynamics based predictions into the optimization of de novo protein designs : Limitations and benefits. / Carvalho, Henrique F; Barbosa, Arménio J M; Roque, Ana C A; Iranzo, Olga; Branco, Ricardo J F.

Methods in Molecular Biology. Vol. 1529 Humana Press Inc, 2017. p. 181-201 (Methods in Molecular Biology; Vol. 1529).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Carvalho HF, Barbosa AJM, Roque ACA, Iranzo O, Branco RJF. Integration of molecular dynamics based predictions into the optimization of de novo protein designs: Limitations and benefits. In Methods in Molecular Biology. Vol. 1529. Humana Press Inc. 2017. p. 181-201. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-6637-0_8