Published March 3, 2023 | Version v1
Dataset Open

Data for manuscript "Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting"

Authors/Creators

  • 1. MSU-DOE Plant Research Laboratory, East Lansing, MI, USA
  • 2. Pacific Northwest National Laboratory, Richland, WA, USA
  • 3. School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
  • 4. Brookhaven National Laboratory, Computational Science Initiative, Upton, NY, USA
  • 5. Rutgers University, Electrical & Computer Engineering, New Brunswick, NJ, USA

Description

The tar file contains the input files for RADICAL augmented MDFF implementation (R-MDFF) for two protein systems, Adenylate Kinase (ADK) and Carbon Monoxide Dehydrogenase (CODH). These examples demonstrate the implementation of R-MDFF using RADICAL-Cybertools to flexibly fit biomolecules in cryo-EM density maps with on-the-fly decision making.

All molecular simulations were performed using CUDA enabled NAMD 2.14 installed on OLCF Summit HPC resource. The CHARMM36 force field parameters were used for the proteins. Synthetic density maps were prepared at 1.8, 3 and 5 Å for ADK and 1.8 and 3 Å for CODH using VMD 1.9.3 software installed on OLCF Summit HPC resource. During the analysis stage, the cross correlation coefficients between density maps and atomic model were computed using VMD 1.9.3 on Summit HPC as part of the R-MDFF workflow.

The source code is publicly available on GitHub: https://github.com/radical-collaboration/MDFF-EnTK

The preprint of this research is submitted on bioRxiv, doi: https://doi.org/10.1101/2021.12.07.471672

To obtain maximum compression of the data, the tar command used to generate this tarball was:

GZIP=-9 tar --exclude='last.pdb' --exclude='*last_from_prev_iter.pdb' --exclude='*old' --exclude='*log' --exclude='*coor' --exclude='*vel' --exclude='*xsc' --exclude='*dcd' --exclude='lastframepdbs_fix' --exclude='*out' --exclude='*sl' --exclude='*rs' --exclude='*prof' --exclude='*err' --exclude='*dx' --exclude='*grid.pdb' --exclude='*txt' -cvzf rmdffv2.tar.gz rmdff-zenodo/

 

Files

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