# 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 The Protein Class and The GEM-PRO Pipeline.

## 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