NatalieQ: a web server for protein-protein interaction network querying.

Area of Science:

• Systems Biology
• Bioinformatics
• Computational Biology

Background:

• Biological systems' complexity necessitates modeling molecular interactions via biological networks.
• Protein-protein interaction (PPI) networks are crucial for understanding cellular processes.
• The Natalie algorithm offers advanced combinatorial optimization for high-quality network alignment.

Purpose of the Study:

• Introduce NatalieQ, a web server for topology-based alignment of query PPI networks to target networks.
• Enable functional annotation transfer and prediction of missing interactions by integrating sequence and network similarity.
• Demonstrate NatalieQ's utility through a case study on the Wnt signaling pathway.

Main Methods:

• Utilizes the Natalie algorithm for network alignment.
• Incorporates both sequence and network topology similarity metrics.
• Web server implementation for user accessibility.

Main Results:

• NatalieQ performs topology-based alignment of protein-protein interaction networks.
• Alignments facilitate the transfer of functional annotations.
• The server successfully predicts putative protein interactions.

Conclusions:

• Topology-based network alignment provides complementary insights to sequence similarity alone.
• NatalieQ effectively predicts potential novel interactions.
• The NatalieQ web server is publicly available for research use.