Published October 2, 2023
| Version Version 1
Dataset
Open
Dataset from "Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations"
Authors/Creators
- 1. LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto
Description
Dataset from "Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations", containing the most relevant simulation output trajectories ran with GROMACS 2021:
1) apo simulations, including wildtype, Y28F, and H228A;
2) holo simulations, including the two tested protonation states for the antibiotic;
3) mutant simulations, including Y18F, H228A, E268Q, and E284Q.
All folders contain the topology file (.top), restraint files (.itp), the initial coordinates file (.gro), and the coordinates after the first minimization (em1.gro). The output trajectories of all replicas (per system) have been concatenated in a single compressed file (.xtc).
Notes
JTSC thanks Fundação para a Ciência e Tecnologia (FCT) for funding through the Scientific Employment Stimulus - Individual Call (ref. CEECIND/01374/2018). This work was produced with the support of the High Performance Computing at the University of Évora (HPCUÉ) and it was funded by FCT I.P. under the project Advanced Computing Project 2022.15843.CPCA.A1, platform Oblivion.
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Related works
- Is referenced by
- Journal article: 10.1021/acs.jcim.3c00962 (DOI)