Shura Hayryan

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We describe a revised and updated version of the program package SMMP (Simple Molecular Mechanics for Proteins) [ SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and inexpensive tool for researchers and students to become familiar with protein simulation techniques.(More)
In the calculation of thermodynamic properties and three-dimensional structures of macromolecules, such as proteins, it is important to have an efficient algorithm for computing the solvent-accessible surface area of macromolecules. Here, we propose a new analytical method for this purpose. In the proposed algorithm we consider the transformation that maps(More)
The folding of the alpha-helix domain hbSBD of the mammalian mitochondrial branched-chain alpha-ketoacid dehydrogenase complex is studied by the circular dichroism technique in absence of urea. Thermal denaturation is used to evaluate various thermodynamic parameters defining the equilibrium unfolding, which is well described by the two-state model with the(More)
In calculating the solvation energy of proteins, the hydration effects, drug binding, molecular docking, etc., it is important to have an efficient and exact algorithms for computing the solvent accessible surface area and the excluded volume of macro-molecules. Here we present a Fortran package based on the new exact analytical methods for computing volume(More)
The determination of the three-dimensional (3D) structure of a protein or peptide is a very important research problem in biological and medical sciences. Anfinsen's experiments (Science 1973, 181, 223) on renaturation of denatured proteins have shown that the native 3D structure of a (small) protein at low (room) temperatures is uniquely determined by its(More)
An efficient combination of the Wang-Landau and transition matrix Monte Carlo methods for protein and peptide simulations is described. At the initial stage of simulation the algorithm behaves like the Wang-Landau algorithm, allowing to sample the entire interval of energies, and at the later stages, it behaves like transition matrix Monte Carlo method and(More)
We present a general thermodynamic picture of the folding of RNA-like heteropolymer based on the basic physical principles. The Hamiltonian of the model includes all characteristic interactions explicitly. A particular attention is paid to the electrostatic interactions whose role in the RNA folding is known to be crucial. In this paper we study RNA folding(More)
The replica technique method is applied to investigate the kinetic behavior of the coarse-grained model for the RNA molecule. A non-equilibrium phase transition of second order between the glassy phase and the ensemble of freely fluctuating structures has been observed. The non-equilibrium steady state is investigated as well and the thermodynamic(More)