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Conformation-dependent sequence design: evolutionary approach

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Abstract.

A new modification of evolutionary approach to sequence design of copolymers has been proposed. A model of step-by-step evolution of a two-letter (HP) copolymer sequence has been studied by means of a coarse-grained Monte Carlo algorithm. The conditions for accepting a change in the primary sequence depend on the spatial conformation of HP-copolymer chain. This leads to a coupling between sequence and conformation and to formation of protein-like conformations and primary sequences (for some values of parameters of the model) independently of initial sequence and/or conformation. Simple theory describing these computer simulation observations is developed.

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Correspondence to A. V. Chertovich.

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Received: 3 September 2003, Published online: 2 March 2004

PACS:

87.15.Aa Theory and modeling; computer simulation - 87.15.Cc Folding and sequence analysis - 82.35.Jk Copolymers, phase transitions, structure - 82.35.Lr Physical properties of polymers

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Chertovich, A.V., Govorun, E.N., Ivanov, V.A. et al. Conformation-dependent sequence design: evolutionary approach. Eur. Phys. J. E 13, 15–25 (2004). https://doi.org/10.1140/epje/e2004-00036-1

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  • DOI: https://doi.org/10.1140/epje/e2004-00036-1

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