Andrzej Sikorski

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A complex, cascaded neural network designed to predict the secondary structure of globular proteins has been developed. Information about the local buried-unburied pattern and the average tendency of the particular types of amino acids to be buried inside the globule were used. Nonspecific information about long distance contact maps was also employed.(More)
The nature of the equilibrium conformational transition from the denatured state to a four-member alpha-helical bundle was studied employing a dynamic Monte Carlo algorithm in which the model protein chain was confined to a tetrahedral lattice. The model chain was allowed to hunt over all phase space, the target native state was not assumed a priori, and no(More)
To help elucidate the general rules of globular protein folding, computer simulations of the conformational transition in model proteins having the left-handed, four-helix bundle motif in which the helices are joined by one or two long loops, as in apoferritin and somatotropin, respectively, have been undertaken. In the context of simple tetrahedral lattice(More)
In the context of reduced protein models, Monte Carlo simulations of three de novo designed helical proteins (four-member helical bundle) were performed. At low temperatures, for all proteins under consideration, protein-like folds having different topologies were obtained from random starting conformations. These simulations are consistent with(More)
The structure of a two-dimensional film formed by adsorbed polymer chains was studied by means of Monte Carlo simulations. The polymer chains were represented by linear sequences of lattice beads and positions of these beads were restricted to vertices of a two-dimensional square lattice. Two different Monte Carlo methods were employed to determine the(More)
A simple model of a polymer brush was constructed. The star polymers with three arms were terminally attached with one arm (the stem) to an impenetrable surface with the other two arms (branches) free. The excluded volume effect was included into the model as the only interaction. Therefore, the system was studied in good solvent conditions. The simulations(More)