ssbio

ssbio integrates protein structural data with genome-scale network reconstructions to construct GEM-PROs (Genome-Scale Models with Protein Structures) and enable structural systems biology analyses.

Key Features:

• Automated GEM-PRO construction: An automated pipeline assembles genome-scale models that incorporate protein structures.
• Third-party program integration: Provides wrappers to invoke third-party programs for computing protein properties from structural data.
• 3D structure-system mapping: Maps and links 3D protein structural information to components of genome-scale network reconstructions.
• Genome-scale handling: Supports processing and integration of structural information across thousands of proteins within large-scale biological networks.

Scientific Applications:

• GEM-PRO generation: Construction of genome-scale models augmented with protein structural data for systems-level analyses.
• Protein property analysis at scale: Computation and incorporation of protein properties across many genes/proteins to study interactions, functions, and dynamics.
• Structure-informed systems biology: Linking molecular 3D structure to network-level behavior and hypotheses in structural systems biology studies.

Methodology:

Implemented in Python, ssbio provides an automated pipeline and wrappers for third-party programs to integrate protein structural data and compute protein properties within genome-scale network reconstructions.