Internal coarse-graining of molecular systems

@article{Feret2009InternalCO,
  title={Internal coarse-graining of molecular systems},
  author={J{\'e}r{\^o}me Feret and Vincent Danos and Jean Krivine and Russell Harmer and Walter Fontana},
  journal={Proceedings of the National Academy of Sciences},
  year={2009},
  volume={106},
  pages={6453 - 6458}
}
Modelers of molecular signaling networks must cope with the combinatorial explosion of protein states generated by posttranslational modifications and complex formation. Rule-based models provide a powerful alternative to approaches that require explicit enumeration of all possible molecular species of a system. Such models consist of formal rules stipulating the (partial) contexts wherein specific protein–protein interactions occur. These contexts specify molecular patterns that are usually… 

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