| abstract |
Abstract Cross-disciplinary approaches to computational biology can yield a number of interesting results. In this talk, one such approach of using formal language theory and symbolic dynamics will be illustrated. The problem chosen for demonstration is generation of spider silk proteins. Spider silk is a material of considerable interest due to its remarkable properties, and a number of attempts are focussed on obtaining this material. Here we show that the essential spider silk like behaviour can be captured in the language of its sequence and one can construct machines to generate it. The generated sequences are shown to have silk like properties and are validated as spider silk using a number of methods. We also show the use of such an approach for detecting/constructing a protein sequences with a given function, fold or having particular domains. In particular, we show how this approach can be used to detect proteins involved in apoptosis, that is, cell death. This approach is far more tractactable than other methods and can be used in a number of contexts some of which would be listed.
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