Work

Molecular Dynamics Trajectory and Validation Dataset for a Repaired Computational Structure Model of Dengue Virus Serotype 1 NS2B/NS3 Protease

Year: 2026

Type: dataset

Abstract: This dataset contains the raw production molecular dynamics trajectory files, system topology, and validation plots for a computationally repaired model of the Dengue Virus Serotype 1 NS2B/NS3 Protease domain (originally derived from wwPDB ID: 3L6P). The system was simulated for 30 nanoseconds in explicit solvent using GROMACS 2026.2 and the CHARMM36 force field to achieve thermodynamic equilibrium. Included files: centered trajectory (xtc), portable run input (tpr), system topology (top), and RMSD/RMSF validation plots. The structural snapshot extracted at 25 ns has been deposited in ModelArchive under entry code ma-b2fty.

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.20331828

Author: Bhowmick, Sumit

Institution: Kalpavriksh

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

OpenAlex ID: W7162013992

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