Towards Inferring Protein Interactions: Challenges and Solutions

  • Ya ZhangEmail author
  • Hongyuan Zha
  • Chao-Hsien Chu
  • Xiang Ji
Open Access
Research Article
Part of the following topical collections:
  1. Advanced Signal Processing Techniques for Bioinformatics


Discovering interacting proteins has been an essential part of functional genomics. However, existing experimental techniques only uncover a small portion of any interactome. Furthermore, these data often have a very high false rate. By conceptualizing the interactions at domain level, we provide a more abstract representation of interactome, which also facilitates the discovery of unobserved protein-protein interactions. Although several domain-based approaches have been proposed to predict protein-protein interactions, they usually assume that domain interactions are independent on each other for the convenience of computational modeling. A new framework to predict protein interactions is proposed in this paper, where no assumption is made about domain interactions. Protein interactions may be the result of multiple domain interactions which are dependent on each other. A conjunctive norm form representation is used to capture the relationships between protein interactions and domain interactions. The problem of interaction inference is then modeled as a constraint satisfiability problem and solved via linear programing. Experimental results on a combined yeast data set have demonstrated the robustness and the accuracy of the proposed algorithm. Moreover, we also map some predicted interacting domains to three-dimensional structures of protein complexes to show the validity of our predictions.


Protein Interaction Abstract Representation Conjunctive Norm Form Domain Level Satisfiability Problem 


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Copyright information

© Zhang et al. 2006

Authors and Affiliations

  • Ya Zhang
    • 1
    • 2
    Email author
  • Hongyuan Zha
    • 3
  • Chao-Hsien Chu
    • 4
  • Xiang Ji
    • 5
  1. 1.Information and Telecommunication Technology CenterThe University of KansasLawrenceUSA
  2. 2.Department of Electrical Engineering and Computer ScienceThe University of KansasLawrenceUSA
  3. 3.Department of Computer Science and Engineering, School of EngineeringPennsylvania State UniversityUniversity ParkUSA
  4. 4.College of Information Sciences and TechnologyPennsylvania State UniversityUniversity ParkUSA
  5. 5.NEC Laboratories America, Inc.CupertinoUSA

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