Molecular dynamics data for UDG enzyme

Dataset

DOI

UDG enzyme-MD simulation.

Initially, the UDG enzyme was solvated using the TIP3P water model, and 0.15 M sodium and chloride ions were added to neutralize the system.

Before running the production MD, minimization and equilibration steps were performed on the UDG enzyme. The final MD production run was conducted on the system for 500 ns to obtain a stable configuration.

The 'input' folder contains the files necessary to run the simulation, while the 'output' folder contains the resulting trajectory.

NAMD, 2.14

charmm, 36

VMD, 1.9.4a57

Identifier
DOI	https://doi.org/10.57745/C5UQ2X
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/C5UQ2X

Provenance
Creator	SARAVANAN, Vinnarasi ; RAOURAOUA, Nessim (ORCID: 0009-0005-5652-684X); BRYSBAERT, Guillaume ; GIORDANO, Stephano ; LENSINK, Marc F. ; CLERI, Fabrizio ; BLOSSEY, Ralf
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 ANR-21-CE45-0032
Rights	etalab 2.0; info:eu-repo/semantics/openAccess; https://spdx.org/licenses/etalab-2.0.html
OpenAccess	true
Contact	BRYSBAERT, Guillaume; SARAVANAN, Vinnarasi

Representation
Resource Type	Dataset
Format	text/plain; application/gzip
Size	507; 35237131518
Version	1.2
Discipline	Life Sciences; Medicine