ProtViewer

A tool to view activity pattern in protein structures. Protein structure visualization is only one application of this tool. One can visualize arbitrary graphs with some activity patterns with this tool.

Website

You can use the tool very easily to visualize activities of certain nodes in graphs. The online-viewer can be used to visualize activity of nodes in a graph. One example is the binding prediction of some model for protein-ligand interactions. The model can output scores defining how much influence a certain node had on the prediction if or if not a certain protein binds to a target or not.

Generating Activity Files

You can easily generate the input files for the online viewer yourself be following the structure described in the "Activity File Structure" section below.

Package Installation

Otherwise, you can install the python package to generate the files using pip

pip install protviewer

and also updating is very easy. Just type

pip install --upgrade protviewer

Package Usage

To use the package and generate the activities for a certain protein, just call

from viewer import view

view(pdb_file, output_dir, activities, distances)

This will generate the json-file inside the output_dir as [pdb_file].json. You can then directly upload this output file to the web service and investigate what your model guided to the decision if a model binds or not.

Activity File Structure

The json-file you input to the online-viewer has to have the following structure

{
  "nodes": [
    "AA_1": {
      "x": ...,
      "y": ...,
      "z": ...,
      "activity": ...,
      "distance": ...,
    }, ...
  ],
  "edges": {
    "start": [
      0, 2, 1, 5, 3, ...
    ],
    "end": [
      2, 1, 5, 3, 6, ...
    ]
  }
}