PubMed · 16218943
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Ettore Appella, Carl W Anderson. 2005. Identifying protein interactions.. https://doi.org/10.1111/j.1742-4658.2005.04944.x
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The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination and replication. Recently, advances have been made in understanding the properties of DNA looping in its natural context and how they propagate to cellular behavior through gene regulation. The result of connecting the molecular properties of DNA looping with cellular physiology measurements indicates that looping of DNA in vivo is much more complex and easier than predicted from current models, and reveals a wealth of previously unappreciated details.
MOTIVATION: Since the knowledge about processes in living cells is increasing, modelling and simulation techniques are used to get new insights into these complex processes. During the last few years, the SBML file format has gained in popularity and support as a means of exchanging model data between the different modelling and simulation tools. In addition to specifying the model as a set of equations, many modern modelling tools allow the user to create and to interact with the model in the form of a reaction graph. Unfortunately, the SBML file format does not provide for the storage of this graph data along with the mathematical description of the model. RESULTS: Therefore, we developed an extension to the SBML file format that makes it possible to store such layout information which describes position and size of objects in the graphical representation. AVAILABILITY: The complete specification can be found on (http://projects.villa-bosch.de/bcb/sbml/ (SBML Layout Extension documentation, 2005). Additionally, a complete implementation exists as part of libSBML (2006, http://www.sbml.org/software/libsbml/).
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