Modelling protein functional domains in signal transduction using Maude.
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.
National Space Biomedical Research Institute, Baylor College of Medicine/NASA Johnson Space Center, Houston, TX 77058-3607, USA. msriram@bcm.tmc.edu
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D000465:Algorithms; D015703:Antigens, CD / Q000737:chemistry / Q000378:metabolism; D017209:Apoptosis / Q000502:physiology; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D008954:Models, Biological; D011381:Programming Languages; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D018124:Receptors, Tumor Necrosis Factor / Q000737:chemistry / Q000378:metabolism; D047888:Receptors, Tumor Necrosis Factor, Type I; D015398:Signal Transduction; D047990:TNF Receptor-Associated Factor 1
D015703:Antigens, CD; D011506:Proteins; D018124:Receptors, Tumor Necrosis Factor; D047888:Receptors, Tumor Necrosis Factor, Type I; D047990:TNF Receptor-Associated Factor 1