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Software for analyzing multiple protein-protein interaction docking solutions, calculating contact regions using mdtraj, and visualizing in useful ways via nglview.

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README.md

Protein-protein interaction docking analysis package

This package utilizes tools from MDtraj and nglview to streamline analysis and visualization of protein-protein interaction docking solutions from servers such as ClusPro, Rosetta, Haddock, Swarmdock, Pie-Dock, etc.

Docking solution files are first converted to an MDtraj-friendly format using mdtraj_converter (this package currently only contains code for ClusPro conversion, but can be easily adapted to other file types). A new directory is created within your working directory entitled "converted_models/" where your MDtraj-friendly files get dumped.

MDtraj is then used to calculate interface residues between two docked structures using get_interface_contacts and contacts_iterator. A distance cutoff is set between all ligand and receptor alpha carbons, with 10 angstroms as default. contacts_iterator is designed to analyze all docking solution files in your working directory. Outputs are aggregate_contacts (all ligand-receptor atom contacts) and aggregate_residues (all ligand-receptor residue contacts), which get saved as callable pickle files in a new folder entitled "summary_data/" in your working directory.

nglview can be used to visually represent individual docking solutions via model_viewer:

Histograms of aggregate docking solution hits by residue, from N- to C-terminus, are also provided via docking_histograms:

Finally, aggregate docking solutions are mapped onto receptor and ligand structures via atom_contacts_parser and heatmap: The heatmap is currently low resolution, separating residues by counts into 0 counts (blue), low counts (yellow), medium counts (orange), and high counts (red), but can easily be tailored to identify particular hotspots of interest.

Next steps:

  • expand conversion capabilities to other server results
  • craft a useful class/OOP architecture for this software:
    • store initial conversion and contact calculations as parent class - remove redundant, slow calculations
    • define children classes that inherit calculations from parent class, construct heatmaps, histograms, etc.
  • expand upon residue analysis tools:
    • more refined heatmap resolution
    • analysis of residue types, more residue metadata

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Software for analyzing multiple protein-protein interaction docking solutions, calculating contact regions using mdtraj, and visualizing in useful ways via nglview.

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