NatalieQ: A web server for protein-protein interaction network querying

Mohammed El-Kebir, Bernd W. Brandt, Jaap Heringa, Gunnar W. Klau

Research output: Contribution to journalArticlepeer-review

Abstract

Background: Molecular interactions need to be taken into account to adequately model the complex behavior of biological systems. These interactions are captured by various types of biological networks, such as metabolic, gene-regulatory, signal transduction and protein-protein interaction networks. We recently developed Natalie, which computes high-quality network alignments via advanced methods from combinatorial optimization.Results: Here, we present NatalieQ, a web server for topology-based alignment of a specified query protein-protein interaction network to a selected target network using the Natalie algorithm. By incorporating similarity at both the sequence and the network level, we compute alignments that allow for the transfer of functional annotation as well as for the prediction of missing interactions. We illustrate the capabilities of NatalieQ with a biological case study involving the Wnt signaling pathway.Conclusions: We show that topology-based network alignment can produce results complementary to those obtained by using sequence similarity alone. We also demonstrate that NatalieQ is able to predict putative interactions. The server is available at: http://www.ibi.vu.nl/programs/natalieq/.

Original languageEnglish (US)
Article number40
JournalBMC Systems Biology
Volume8
Issue number1
DOIs
StatePublished - Apr 1 2014
Externally publishedYes

Keywords

  • Network alignment
  • Protein-protein interaction
  • Sequence similarity
  • Topology
  • Wnt signaling pathway

ASJC Scopus subject areas

  • Structural Biology
  • Modeling and Simulation
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

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