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:

Provide an easy way to map genes to their encoded proteins sequences and structures
Directly link structures to genome-scale SBML models
Prepare structures for downstream analyses, such as their use in molecular modeling software
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].