Molecular dynamics data for DNA base flipping

DOI

DNA base flipping trajectory files. Initial state is a double stranded DNA containing a thymine mutated to a uracil. Uracil is then flipped out according to a 100ns simulation. The DNA structure was created with the w3DNA tool, with a uracil replacing thymine in position 12. The structure was solvated with tip3p water model and 0.15 mol sodium and chloride added to neutralize the system. Minimization, equilibration and production were performed on the system to obtain a stable configuration. Then a metadynamic simulation was run for uracil base flipping using the NAMD tool, with charmm36 force field. The 'input' folder contains the input files to run the simulation. The 'output' folder contains the trajectory.

NAMD, 2.14

charmm, 36

VMD, 1.9.4a57

Identifier
DOI https://doi.org/10.57745/30ABBY
Related Identifier IsCitedBy https://doi.org/10.1038/s41598-025-91705-6
Metadata Access https://entrepot.recherche.data.gouv.fr/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.57745/30ABBY
Provenance
Creator SARAVANAN, Vinnarasi ORCID logo; RAOURAOUA, Nessim (ORCID: 0009-0005-5652-684X); BRYSBAERT, Guillaume ORCID logo; GIORDANO, Stephano ORCID logo; LENSINK, Marc F. ORCID logo; CLERI, Fabrizio ORCID logo; BLOSSEY, Ralf ORCID logo
Publisher Recherche Data Gouv
Contributor BRYSBAERT, Guillaume; SARAVANAN, Vinnarasi; Centre national de la recherche scientifique; Université de Lille; Entrepôt-Catalogue Recherche Data Gouv
Publication Year 2024
Funding Reference Agence nationale de la recherche
Rights etalab 2.0; info:eu-repo/semantics/openAccess; https://spdx.org/licenses/etalab-2.0.html
OpenAccess true
Contact BRYSBAERT, Guillaume (CNRS - Personnels des unités); SARAVANAN, Vinnarasi (CNRS - Personnels des unités)
Representation
Resource Type Dataset
Format application/gzip; text/plain
Size 13267700458; 722
Version 2.2
Discipline Life Sciences; Medicine