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

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.


Experiment data files

Steps to reproduce

  1. Docking of atrazine to the lignin peroxidase ligand access channel's surface. More details:

  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


    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

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Szent Istvan University Faculty of Agricultural and Environmental Sciences


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


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