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Add description file for the systems.
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ludovicaisa committed Oct 14, 2024
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# Flexible Protein-Ligand Docking Paper's files

This repository contains input simulations files from
["Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking"](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0228461).
which are:

1. ** 2g5n_complex.xml ** : trypsin and indole-amidine, based on PDB file 2G5N.
An 800 kJ/mol/nm2 restraint was added to all backbone atoms of trypsin.
2. ** hiv1_complex.xml ** : HIV-1 protease and amprenavir, based on on PDB file 1HPV.
An 800 kJ/mol/nm2 was applied to all backbone atoms of HIV-1 complex, excluding those which
make up the flaps which gate the active site (defined as residues 49 to 55 in chain A and
residues 48 to 54 in chain B).
3. ** 6hcx_complex_no_restrains.xml ** : neuraminidase and zanamivir, based on PDB file 6HCX.
No restraint is applied to the complex.

All files have been converted from NarupaXR (.xml) to Nanover iMD-VR (.xml)

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