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.
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.|Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
authors.forename: Henrique F
authors.initials: HF
authors.lastname: Carvalho
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
authors.forename: Arménio J M
authors.initials: AJ
authors.lastname: Barbosa
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
authors.forename: Ana C A
authors.initials: AC
authors.lastname: Roque
authors.affiliation: iSm2 UMR CNRS 7313, Aix-Marseille UniversitÕ / CNRS, 13397, Marseille, France. olga.iranzo@univ-amu.fr.
authors.forename: Olga
authors.initials: O
authors.lastname: Iranzo
authors.affiliation: UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal. ricardo.branco@fct.unl.pt.
authors.forename: Ricardo J F
authors.initials: RJ
authors.lastname: Branco
mesh_terms: D019295:Computational Biology / Q000379:methods*; D004798:Enzymes / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D012984:Software; D064878:Web Browser
chemical_list: D004798:Enzymes; D011506:Proteins
keywords: Elastic network models; Internal molecular dynamics; Normal mode analysis; Principal component analysis; Protein essential dynamics