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 proteins to sequences and structures
- Directly link structures to genome-scale SBML models
- Prepare structures for downstream analyses, such as their use in molecular modeling software
Example questions you can 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?
- and more...
First install NGLview using pip:
pip install nglview
Then install ssbio:
pip install ssbio
pip install ssbio --upgrade
pip uninstall ssbio
Currently, use of this package can be cited by our 2016 paper in BMC Systems Biology , which details the GEM-PRO pipeline. The manuscript for the
ssbio package itself is in preparation at this moment.
|||Brunk, E.*, Mih, N.*, Monk, J., Zhang, Z., O’Brien, E. J., Bliven, S. E., Bourne, P. E., Palsson, B. O. (2016). Systems biology of the structural proteome. BMC Systems Biology, 10(1), 26. http://doi.org/10.1186/s12918-016-0271-6. *Authors contributed equally.|
- Getting Started
- The StructProp Class
- The Protein Class
- The GEM-PRO Pipeline
- The ATLAS Pipeline
- Python API