Code and analysis for the publication "Comparing Multislice Projections of MD simulations with CryoEM Exposes Structural Prediction Errors"
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2025
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| _version_ | 1866901897436200960 |
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| author | Natale, Andrew Mohammed, Arshad Lincoff, James Ophus, Colin Grabe, Michael Frost, Adam Moss, Frank |
| author_facet | Natale, Andrew Mohammed, Arshad Lincoff, James Ophus, Colin Grabe, Michael Frost, Adam Moss, Frank |
| contents | <p dir="auto">Code, simulation ensembles, and analysis associated with the publication:</p> <p dir="auto">Mohammed A., Lincoff J., Natale A., Ophus C., Grabe M., Frost R., & Moss F. Comparing Multislice Projections of MD simulations with CryoEM Exposes Structural Prediction Errors. 2026 Biophysical Journal.</p> <p dir="auto"> </p> <p dir="auto">The archive file 'multislice_membrane_md-2.tar.gz' contains:</p> <p dir="auto">Python notebooks (*multislice_preprocess.ipynb) in the top level of the archive repo load AA or backmapped-CG simulation snapshots and produce PDB files ready for input to multislice.</p> <p dir="auto">And subdirectories for the following:</p> <p dir="auto">'multislice_matlab_code' - matlab code for running the multislice pipeline on prepared simulation snapshots.</p> <p dir="auto">'molmap_histogram_analysis' - contains python notebooks to generate figures from calculations of lipid particle histograms for comparing lipid distributions between simulations for flat and curved bilayer simulations. Also for checking membrane shape differences between simulated conditions - this uses the 'molmap' approach as in ChimeraX to generate simulated density maps by blurring each atom with a Gaussian scaled by its expected scattering value. These maps can be used to quickly compare shapes, but lack some of the features of real maps that are captured by the full multislice approach.</p> <p dir="auto">'stability_analysis' - contains python notebooks for assessing simulation properties to verify that flat and curved bilayer MD simulations ran as expected.</p> <p dir="auto">'backmap_scripts_data' - contains code to apply Martini3 to CHARMM36 lipid backmapping procedure (custom, but inspired by the published 'backward' approach) to the flat and curved bilayer MD simulations associated with this paper.</p> <p dir="auto"> </p> <p dir="auto">The archive file '175_200.zip' contains PDB format coordinate files of frames from time 175-200 ns of the 200 ns all-atom ESCRT tubule MD simulation.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17808731 |
| institution | Zenodo |
| language | eng |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Code and analysis for the publication "Comparing Multislice Projections of MD simulations with CryoEM Exposes Structural Prediction Errors" Natale, Andrew Mohammed, Arshad Lincoff, James Ophus, Colin Grabe, Michael Frost, Adam Moss, Frank CryoEM Molecular Dynamics Simulation Biological membranes Multislice wave propagation CHARMM36 Martini3 <p dir="auto">Code, simulation ensembles, and analysis associated with the publication:</p> <p dir="auto">Mohammed A., Lincoff J., Natale A., Ophus C., Grabe M., Frost R., & Moss F. Comparing Multislice Projections of MD simulations with CryoEM Exposes Structural Prediction Errors. 2026 Biophysical Journal.</p> <p dir="auto"> </p> <p dir="auto">The archive file 'multislice_membrane_md-2.tar.gz' contains:</p> <p dir="auto">Python notebooks (*multislice_preprocess.ipynb) in the top level of the archive repo load AA or backmapped-CG simulation snapshots and produce PDB files ready for input to multislice.</p> <p dir="auto">And subdirectories for the following:</p> <p dir="auto">'multislice_matlab_code' - matlab code for running the multislice pipeline on prepared simulation snapshots.</p> <p dir="auto">'molmap_histogram_analysis' - contains python notebooks to generate figures from calculations of lipid particle histograms for comparing lipid distributions between simulations for flat and curved bilayer simulations. Also for checking membrane shape differences between simulated conditions - this uses the 'molmap' approach as in ChimeraX to generate simulated density maps by blurring each atom with a Gaussian scaled by its expected scattering value. These maps can be used to quickly compare shapes, but lack some of the features of real maps that are captured by the full multislice approach.</p> <p dir="auto">'stability_analysis' - contains python notebooks for assessing simulation properties to verify that flat and curved bilayer MD simulations ran as expected.</p> <p dir="auto">'backmap_scripts_data' - contains code to apply Martini3 to CHARMM36 lipid backmapping procedure (custom, but inspired by the published 'backward' approach) to the flat and curved bilayer MD simulations associated with this paper.</p> <p dir="auto"> </p> <p dir="auto">The archive file '175_200.zip' contains PDB format coordinate files of frames from time 175-200 ns of the 200 ns all-atom ESCRT tubule MD simulation.</p> |
| title | Code and analysis for the publication "Comparing Multislice Projections of MD simulations with CryoEM Exposes Structural Prediction Errors" |
| topic | CryoEM Molecular Dynamics Simulation Biological membranes Multislice wave propagation CHARMM36 Martini3 |
| url | https://doi.org/10.5281/zenodo.17808731 |