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- A V Badasyan, A V Grigoryan, E Sh Mamasakhlisov, A S Benight, V F Morozov
- The Journal of chemical physics
- 2005

A microscopic Potts-like one-dimensional model with many-particle interactions is developed to construct a statistical mechanical description of the melting of heterogeneous sequence duplex DNA. For this model, referred as the generalized model of polypeptide chains (GMPC), a closed-form expression for the free energy is derived. The characteristic equation… (More)

- A V Grigoryan, E Sh Mamasakhlisov, T Yu Buryakina, A V Tsarukyan, A S Benight, V F Morozov
- The Journal of chemical physics
- 2007

A microscopic Potts-like one-dimensional model with many particle interactions [referred as the generalized model of polypeptide chains (GMPCs)] is developed to investigate cooperativity of DNA sequence dependent melting. For modeling sequence, regular homogeneous sequences were arranged in heterogeneous blocks of various lengths. Within the framework of… (More)

- A. V. Grigoryan, Irina Kufareva, Maxim Totrov, Ruben Abagyan
- Journal of Computer-Aided Molecular Design
- 2010

Similarity of compound chemical structures often leads to close pharmacological profiles, including binding to the same protein targets. The opposite, however, is not always true, as distinct chemical scaffolds can exhibit similar pharmacology as well. Therefore, relying on chemical similarity to known binders in search for novel chemicals targeting the… (More)

A simplified model for the closed circular DNA (ccDNA) is proposed to describe some specific features of the helix-coil transition in such molecule. The Hamiltonian of ccDNA is related to the one introduced earlier for the linear DNA. The basic assumption is that the reduced energy of the hydrogen bond is not constant through the transition process but… (More)

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