CASE STUDY
Structural Systems Biology and Genome-Scale Modeling (GEM-PRO)
Enabled genome-scale integration of protein structures, bridging the gap between sequence data and functional biological systems modeling.
Situation
The client required a method to connect genomic data with protein structure information to better understand biological systems and disease mechanisms.
Solution
Developed computational frameworks for structural systems biology that integrated genome-scale datasets with protein structure and interaction modeling.
OUTCOMES
29% deeper
pathway-level disease insight
4,800 proteins
within integrated structural models
Prepared targets
for translational teams
Challenges
Integration
- •Disconnected genomic datasets
- •Limited structure linkage
Modeling
- •Incomplete systems-level models
- •Missing phenotype connections
Solutions
01
Automated GEM-PRO Generation
Automated generation of genome-scale models enriched with protein structures (GEM-PROs)
- Generated genome-scale structural model datasets
- Linked sequence and structure representations
- Enabled scalable systems-level biological modeling
02
Interaction Network Integration
Integration of protein–protein interaction networks.
- Incorporated interaction networks into models
- Improved pathway-level biological insight
- Enabled multi-protein systems analysis
03
Thermodynamic Modeling Frameworks
Thermodynamic and biophysical modeling of molecular systems.
- Modeled molecular stability and energetics
- Supported phenotype-level interpretation workflows