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 at :ref:`protein` and :ref:`gempro`.

Citation

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

[1]	Mih, N. et al. ssbio: A Python Framework for Structural Systems Biology. bioRxiv 165506 (2017). doi:10.1101/165506