@inbook{7fbef8e9e9a54ad5b53ce602a2a7dcd6,
title = "Integration of molecular dynamics based predictions into the optimization of de novo protein designs: Limitations and benefits",
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.",
keywords = "Elastic network models, Internal molecular dynamics, Normal mode analysis, Principal component analysis, Protein essential dynamics",
author = "Carvalho, {Henrique F} and Barbosa, {Arm{\'e}nio J M} and Roque, {Ana C A} and Olga Iranzo and Branco, {Ricardo J F}",
note = "Sem PDF. The authors thank the financial support from Funda??o para a Ci?ncia 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 Ci?ncias 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).",
year = "2017",
doi = "10.1007/978-1-4939-6637-0_8",
language = "English",
volume = "1529",
series = "Methods in Molecular Biology",
publisher = "Humana Press",
pages = "181--201",
booktitle = "Methods in Molecular Biology",
address = "United States",
}