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ZENODO
Dataset . 2023
License: CC BY
Data sources: ZENODO
ZENODO
Dataset . 2023
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2023
License: CC BY
Data sources: Datacite
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Gaussian-accelerated Molecular Dynamics simulations of CCR8-CCL1-Gprotein complex in a POPC lipid bilayer

Authors: Nicoludis, John;

Gaussian-accelerated Molecular Dynamics simulations of CCR8-CCL1-Gprotein complex in a POPC lipid bilayer

Abstract

Gaussian-accelerated Molecular Dynamics simulations of the CCR8-CCL1-Gprotein complex in a POPC lipid bilayer. Simulation system was prepared with OpenMM v7.7 and simulations were performed using the GaMD-OpenMM package (https://github.com/MiaoLab20/gamd-openmm) with a modification to include the MDTraj h5 file formate reporter as the output file format. These simulations were then converted to pdb topologies and dcd trajectories using MDTraj. Files include: CCL1_CCR8_noSer23_oriented_repaired1_system.pdb : system topology CCL1_CCR8_config.xml : config for running GaMD-OpenMM CCL1_CCR8_N_1ns_imaged_structure.pdb : initial topology/structure CCL1_CCR8_N_1ns_imaged_trajectory.dcd : trajectory file Simulations can be loaded in python using MDTraj: import mdtraj trj = mdtraj.load(, top=)

Related Organizations
Keywords

enhanced MD, MD simulations, GPCR, GaMD, membrane proteins, molecular dynamics

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
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.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average