Bioinformatics
Bioinformatics
5 years ago

ssbio: A Python Framework for Structural Systems Biology.

Anand Sastry, Zhen Zhang, Alfonso Valencia, Edward Catoiu, Nathan Mih, Erol Kavvas, Bernhard O Palsson, Jonathan M Monk, Elizabeth Brunk, Ke Chen
Working with protein structures at the genome-scale has been challenging in a variety of ways. Here, we present ssbio, a Python package that provides a framework to easily work with structural information in the context of genome-scale network reconstructions, which can contain thousands of individual proteins. The ssbio package provides an automated pipeline to construct high quality genomescale models with protein structures (GEM-PROs), wrappers to popular third-party programs to compute associated protein properties, and methods to visualize and annotate structures directly in Jupyter notebooks, thus lowering the barrier of linking 3D structural data with established systems workflows.

Publisher URL: http://doi.org/10.1093/bioinformatics/bty077

DOI: 10.1093/bioinformatics/bty077

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