Abstract
Folding properties of two simple off-lattice protein models in two and three dimensions, respectively, are analyzed numerically by using the simulated-tempering method. Both models have two types of “amino acids”, hydrophobic and hydrophilic. In the two-dimensional model, a total of 300 randomly selected sequences with 20 monomers are studied. About 10% of these meet criteria for good folders. A statistical analysis of the distribution of hydrophobic monomers along the chains is performed, both for the good folders in this model and for functional proteins. This analysis convincingly shows that the hydrophobicity distribution is nonrandom for functional proteins. Furthermore, qualitatively similar deviations from randomness are found for good folders in the model. The study of the three-dimensional model demonstrates the importance of local interactions.
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© 1998 Springer-Verlag
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Irbäck, A. (1998). Simulations of toy proteins. In: Meyer-Ortmanns, H., Klümper, A. (eds) Field Theoretical Tools for Polymer and Particle Physics. Lecture Notes in Physics, vol 508. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0106883
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DOI: https://doi.org/10.1007/BFb0106883
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