Structure of a lignin peroxidase ligand access channel-atrazine complex after molecular dynamics simulation

Published: 26 Sep 2017 | Version 1 | DOI: 10.17632/b2wn6fdcj4.1
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Description of this data

State and contacts of the lignin peroxidase ligand access channel-atrazine complex after 5 ns molecular dynamics. The simulation was performed with NAMD (CHARMM36 force field). The input structure for the simulation was created by molecular docking.

See: http://dx.doi.org/10.17632/dvjms8448j.1

Experiment data files

Steps to reproduce

  1. Docking of atrazine to the lignin peroxidase ligand access channel's surface. More details:
    http://dx.doi.org/10.17632/dvjms8448j.1

  2. Save the file as a protein-ligand complex with AutoDockTools.

  3. Energy minimization with NAMD (20-30 ps).

  4. Molecular dynamics with NAMD: solvation and neutralization, 5 ns, NPT microcanonical ensemble, Periodic Boundary Conditions and Particle Mesh Ewald electrostatics, CHARMM36 force field.

Latest version

Previous versions

  • Version 1

    2017-09-26

    Published: 2017-09-26

    DOI: 10.17632/b2wn6fdcj4.1

    Cite this dataset

    Ecker, János; Fülöp, László (2017), “Structure of a lignin peroxidase ligand access channel-atrazine complex after molecular dynamics simulation”, Mendeley Data, v1 http://dx.doi.org/10.17632/b2wn6fdcj4.1

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Institutions

Szent Istvan University Faculty of Agricultural and Environmental Sciences

Categories

Three-Dimensional Graphics, Enzyme Structure, Enzyme Structure-Function Relationship, Ligand Binding, Three-Dimensional Reconstruction of Biomoleculair Structures

Licence

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The files associated with this dataset are licensed under a Creative Commons Attribution 4.0 International licence.

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