ssbio 0.9.9.2

Tools to enable 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 currently be found and cited at bioRxiv [1].

[1]

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