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A Fortran package is presented which provides useful routines for molecular simulation of proteins within the standard geometry model. Highly efficient algorithms for the calculation of energy and its derivatives are implemented. A set of energy minimization routines and modern Monte Carlo algorithms are added. Three different parameter sets are used to… (More)

- Frank Eisenmenger, Ulrich H. E. Hansmann, Shura Hayryan, Chin-Kun Hu
- Computer Physics Communications
- 2006

We describe a revised and updated version of the program package SMMP (Simple Molecular Mechanics for Proteins) [F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan, C.-K. Hu, Comput. Phys. Comm. 138 (2001) 192–212]. SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and… (More)

- Maksim Kouza, Chi-Fon Chang, +4 authors Chin-Kun Hu
- Biophysical journal
- 2005

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)

- Shura Hayryan, Chin-Kun Hu, Jaroslav Skrivánek, Edik Hayryan, Imrich Pokorný
- Journal of Computational Chemistry
- 2005

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)

- Shura Hayryan, Chin-Kun Hu, Shun-Yun Hu, Rung-Ji Shang
- Journal of Computational Chemistry
- 2001

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)

- Ján Busa, Jozef Dzurina, +6 authors Ming-Chya Wu
- Computer Physics Communications
- 2005

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 macromolecules. Here we present a Fortran package based on the new exact analytical methods for computing volume… (More)

- Ján Busa, Shura Hayryan, Chin-Kun Hu, Jaroslav Skrivánek, Ming-Chya Wu
- Computer Physics Communications
- 2010

Article history: Received 22 March 2010 Received in revised form 20 August 2010 Accepted 24 August 2010 Available online 17 September 2010

- Ruben Ghulghazaryan, Shura Hayryan, Chin-Kun Hu
- Journal of Computational Chemistry
- 2007

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)

- Yevgeni Sh Mamasakhlisov, Shura Hayryan, V F Morozov, Chin-Kun Hu
- Physical review. E, Statistical, nonlinear, and…
- 2007

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)

- Shura Hayryan, Chin-Kun Hu, Edik Hayryan, Imrich Pokorný
- International Conference on Computational Science
- 2003