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Dataset . 2020
License: CC BY
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ZENODO
Dataset . 2020
License: CC BY
Data sources: ZENODO
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ZENODO
Dataset . 2020
License: CC BY
Data sources: Datacite
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MD simulation data: An Entropic Safety Catch Controls Hepatitis C Virus Entry and Antibody Resistance

Authors: Shepherd, Adrian John; Stejskal, Lenka; Grove, Joe;

MD simulation data: An Entropic Safety Catch Controls Hepatitis C Virus Entry and Antibody Resistance

Abstract

Background Equilibration, relaxation and production runs were performed on GPUs using the CUDA version of PMEMD in AMBER 16 and AMBER ff14SB force field. Minimisation steps were performed on a CPU using PMEMD in AMBER 16 and the AMBER ff14SB force field. All software is available from http://ambermd.org/. Contents There are three tarball (.tar.gz) files containing the core simulation data: one for wild type (WT), the second for the I438V A524T mutant and the third for the S449P mutant. Each contains: 1. a source PDB (.pdb) file 2. Five AMBER trajectory (.nc) files for five independent MD simulations, numbered 1 to 5. Note: each of these files is over 2GB. There is an additional tarball containing the control files and scripts used for running the MD simulations: 1. Multiple control (.ctl) files numbered 1 to 10 that are used to minimize (min prefix), relax (rel prefix) and equilibrate (equ prefix) the model 2. Executable do_md that performed all the minimisation, relaxation and equilibration steps 3. control file prod.ctl used for the production run 4. Executable run_prod that was used to perform the production run 5. Two control files (prod_short.ctl and prod_short_2.ctl) for the short runs used to de-correlate the simulation for the independent runs 6. Executable run_short and run_short_2 used to carry out the de-correlated production runs.

Related Organizations
Keywords

hepatitis C virus, MD simulations, E2 glycoprotein, HCV, molecular dynamics

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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
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influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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