These scripts demonstrate the use of IMP in the modeling of the human LINE1 ORF2p protein using diverse types of data.

List of files and directories:

• dependencies\environment.yml : Files required to deploy a conda environment to reproduce the modeling and analysis

• md : Run and output files for molecular dynamics simulations

• data contains all relevant data

  • ORF2p.fasta : Reference protein sequence

  • af_apo_final_lowpass_4.5.pdb : AlphaFold2 model of ORF2p aligned to the APO cryo-em density map

• data_gmm\* GMM representation of the selected fragments of the APO cryo-em density map

• data_npc\negative_stain 2D Negative stain EM images from RNA:DNA and RNA datasets

• data_npc\xls Chemical cross-links and predicted restraints used for modeling

• modeling

  • run_stub\sample_orf2p_mmcif.py Template script to rerun the modeling
  • run_* Modeling output used in the publication

• analysis Output from the SAMPCON analysis pipeline

• validation Validation of modeling results with EM2D data that were not used for sampling

  • ORF2p_em2d_validation.ipynb Jupyter notebook with the validation code and results
  • validation\output Best-fitting models and various figures used in the publication

!NB: Due to size limitations following data available only on Zenodo

• md\*\run_*\md_nojump_fit.xtc - Output MD trajectories
• validation\output\em2d_validation.dump - Binary (dill) dump of EM2D validation data including projections, coordinates, and scores

Information

Author(s): Arthur Zalevsky

License: CC-BY-SA-4.0. This work is freely available under the terms of the Creative Commons Attribution-ShareAlike 4.0 International License.