Applications of Pathway Logic Modeling to Target Identification

  • Anupama Panikkar
  • Merrill Knapp
  • Huaiyu Mi
  • Dave Anderson
  • Krishna Kodukula
  • Amit K. Galande
  • Carolyn Talcott
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7000)


To explore the role of proteases in pathogenesis and as potential drug targets we need to elucidate their function and effect on biological networks. In this paper, we describe the application of Pathway Logic (PL) ( ) to the symbolic modeling of the interaction networks of proteases of Gram-positive bacteria and the use of Pathway Logic Assistant tool (PLA) to browse and query these models. Pathway Logic is a systems biology approach to biological processes as integrated systems rather than isolated parts based on formal methods and rewriting logic. These models are developed using Maude, a formal language and tool set based on rewriting logic. We show how this approach can be used to represent and analyze systems at multiple levels of details. The Pathway Logic Assistant tool enables us to identify key proteases and regulatory molecules – ‘choke points’ by comparing different pathways or networks within and across species and to predict how these molecules, if inhibited or avoided would affect the pathway or network.


Target Identification Potential Drug Target Pilus Assembly Heme Transport Algebraic Data Type 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Anupama Panikkar
    • 1
  • Merrill Knapp
    • 3
  • Huaiyu Mi
    • 2
  • Dave Anderson
    • 1
  • Krishna Kodukula
    • 1
  • Amit K. Galande
    • 1
  • Carolyn Talcott
    • 2
  1. 1.Center for Advanced Drug ResearchSRI InternationalHarrisonburgUSA
  2. 2.Computer Science LabSRI InternationalMenlo ParkUSA
  3. 3.Biosciences DivisionSRI InternationalMenlo ParkUSA

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