Modelling protein functional domains in signal transduction using Maude
An informatics research scientist at the National Space Biomedical Research Institute and an adjunct assistant professor at the School of Health Information Sciences, University of Texas. He has over 18 years of experience in biomedical research. His current research interests include systems biology, healthcare informatics and algorithmic medicine.
M. G. Sriram, National Space Biomedical Research Institute, Baylor College of Medicine/NASA Johnson Space Center, 2101 NASA Rd 1, SD6, Houston, TX 77058-3607, USA Tel: +1 281 483 9057 Fax: +1 281 483 2224 E-mail: msriram{at}bcm.tmc.edu
Modelling of protein—protein interactions in signal transduction is receiving increased attention in computational biology. This paper describes recent research in the application of Maude, a symbolic language founded on rewriting logic, to the modelling of functional domains within signalling proteins. Protein functional domains (PFDs) are a critical focus of modern signal transduction research. In general, Maude models can simulate biological signalling networks and produce specific testable hypotheses at various levels of abstraction. Developing symbolic models of signalling proteins containing functional domains is important because of the potential to generate analyses of complex signalling networks based on structure—function relationships.
Keywords: Maude, protein—protein interaction, protein functional domains, pathway logic, signalling complex
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  W. S. Hlavacek, J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka, and W. Fontana Rules for Modeling Signal-Transduction Systems Sci. Signal., July 18, 2006; 2006(344): re6 - re6. [Abstract] [Full Text] [PDF]
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