ssbio: A Framework for Structural Systems Biology

Introduction

This Python package provides a collection of tools for people with questions in the realm of structural systems biology. The main goals of this package are to:

  1. Provide an easy way to map genes to their encoded proteins sequences and structures
  2. Directly link structures to genome-scale SBML models
  3. Prepare structures for downstream analyses, such as their use in molecular modeling software
  4. Demonstrate fully-featured Python scientific analysis environments in Jupyter notebooks

Example questions you can (start to) answer with this package:

  • How can I determine the number of protein structures available for my list of genes?
  • What is the best, representative structure for my protein?
  • Where, in a metabolic network, do these proteins work?
  • Where do popular mutations show up on a protein?
  • How can I compare the structural features of entire proteomes?
  • How can I zoom in and visualize the interactions happening in the cell at the molecular level?
  • How do structural properties correlate with my experimental datasets?
  • How can I improve the contents of my model with structural data?
  • and more…

Installation

First install NGLview using pip:

pip install nglview

Then install ssbio:

pip install ssbio

Updating

pip install ssbio --upgrade

Uninstalling

pip uninstall ssbio

Dependencies

See: Software Installations for additional programs to install. Most of these additional programs are used to predict or calculate properties of proteins.

Tutorials

Check out some Jupyter notebook tutorials for a single Protein and or for many in a GEM-PRO model.

Citation

The manuscript for the ssbio package can be found and cited at [1].

[1]Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z, Palsson BO. ssbio: A Python Framework for Structural Systems Biology. bioRxiv. 2017. p. 165506. https://doi.org/10.1101/165506

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