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 proteins to 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

Example questions you can 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?
  • 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.

Tutorials

Check out some Jupyter notebook tutorials at The Protein Class and The GEM-PRO Pipeline.

Citation

Currently, use of this package can be cited by our 2016 paper in BMC Systems Biology [1], which details the GEM-PRO pipeline. The manuscript for the ssbio package itself is in preparation at this moment.

[1]Brunk, E.*, Mih, N.*, Monk, J., Zhang, Z., O’Brien, E. J., Bliven, S. E., Bourne, P. E., Palsson, B. O. (2016). Systems biology of the structural proteome. BMC Systems Biology, 10(1), 26. http://doi.org/10.1186/s12918-016-0271-6. *Authors contributed equally.