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Updated: Aug 25, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Conformation-dependent sequence design: evolutionary approach
A V Chertovich1, E N Govorun, V A Ivanov
1Physics Department, Moscow State University, 119992, Moscow, Russia. chertov@polly.phys.msu.ru
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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