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Comparison of allosteric signaling in DnaK and BiP using mutual information between simulated residue conformations

Citation

Schneider, Markus; Antes, Iris (2022), Comparison of allosteric signaling in DnaK and BiP using mutual information between simulated residue conformations, Dryad, Dataset, https://doi.org/10.5061/dryad.1g1jwstzs

Abstract

Molecular Dynamics trajectories of the Hsp70 chaperones DnaK and BiP. System configurations include DnaK or BiP bound to ATP, ATP exchanged to ADP, or the NRLLLTG peptide.

Methods

Molecular Dynamics simulations were created using the AMBER software and processed using CPPTRAJ from the AmberTools software suite.

Usage Notes

The .prmtop file is a text file as used by the AMBER software for molecular dynamics simulations and contains the topology of the molecular system. Any text editor should be able to read the file, though it is designed towards being used by the program.

The .nc file is a binary file format for trajectories created by the AMBER software.

.prmtop and .nc files can be read by the program CPPTRAJ (of the AmberTools software suite) or molecular viewers like VMD. Both AmberTools and VMD are free to download and use.

Funding

Deutsche Forschungsgemeinschaft, Award: SFB1035/A10

Deutsche Forschungsgemeinschaft, Award: SFB749/C08