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Add description file for the systems.
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# Flexible Protein-Ligand Docking Paper's files | ||
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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: | ||
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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. | ||
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All files have been converted from NarupaXR (.xml) to Nanover iMD-VR (.xml) |