Calabretta, R., Nolfi, S., and Parisi, D. 1995. An artificial life model for predicting the tertiary structure of unknown proteins that emulates the folding process. In Moran, F., Moreno, A., Merelo, J.J., and Chacon, P. eds. Lecture notes in artificial intelligence: advances in artificial life., 862-875.  Home/Search   Document Details and Download   Summary   Related Articles   Check

....these results do not account for the three dimensional structure of the molecules; its prediction still constitutes a great unresolved challenge. Previous optimisation techniques for deriving the tertiary structure of proteins [9] 10] have also produced limited results. More recent attempts [8] use real protein helices as test cases to derive a folding matrix that is evolved through a genetic algorithm. This method has been applied to a fragment of the protein crambin made of 13 amino acids and with one alpha helix. Its aim is to reproduce the folding process itself by discovering the ....

....energy for each molecule: backbone interactions V 1 between bonded residues and interactions V 2 between non bonded residues; the former will be independent of the amino sequence while the latter will depend on the residues and their properties. For this type of interaction we can assume (see [8] and references within) that the main force responsible for driving the folding process is the hydrophobicity or aversion for water for nonpolar molecular residues. This force dominates the Van der Waals interactions between dipoles, hydrogen bond interactions between two electronegative atoms ....

R Calabretta, S Nolfi and D Parisi, "An Artificial Life model for predicting the Tertiary Structure of unknown proteins that emulates the folding process", Proc. of Third European Conference of Artificial Life, Granada, 1995.

....level, each gene codifies for a specific protein. The sequence of amino acids for each protein, as it is codified exactly in DNA, contains all the information to determine the three dimensional structure on which the function of that protein finally depends (see for instance Creighton 1993 and Calabretta, Nolfi, and Parisi 1995). As stressed by Doolittle and Bork (1993) proteins are often composed by a limited group of modular elements (domains) that have spread and multiplied during evolution in ways that are starting to be understood. At the phenotypic level evolutionary biologists recognize homologous and analogous ....

Calabretta, R., Nolfi, S., and Parisi, D. 1995. An artificial life model for predicting the tertiary structure of unknown proteins that emulates the folding process. In Moran, F., Moreno, A., Merelo, J.J., and Chacon, P. eds. Lecture notes in artificial intelligence: advances in artificial life., 862-875.

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