ssbio: A Framework for Structural Systems Biology¶
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…
First install NGLview using pip:
pip install nglview
Then install ssbio:
pip install ssbio
pip install ssbio --upgrade
pip uninstall ssbio
The manuscript for the
ssbio package can be found and cited at .
|||Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z, Palsson BO. ssbio: A Python Framework for Structural Systems Biology. bioRxiv. 2017. p. 165506. https://doi.org/10.1101/165506|
Table of Contents¶
- Getting Started
- The GEM-PRO Pipeline
- The Protein Class
- Python API