Role of stacking interactions in the binding sequence preferences of DNA bis-intercalators: insight from thermodynamic integration free energy simulations

By Marco Esther   Negri Ana   Luque F. Javier   Gago Federico  

Nucleic Acids Research, Vol. 33, Iss. 19, 2005-01 ,pp. : 6214-6224

Oxford University Press

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Insights into the specific binding site of adenosine to the Stx2, the protein toxin from Escherichia coli O157:H7 using molecular dynamics simulations and free energy calculations

By Niu Xiaodi   Wang Xin   Wang Hongsu   Gao Xiaohan   Wang Yanan   Wang Song  

Molecular Simulation, Vol. 39, Iss. 3, 2013-03 ,pp. : 199-205

Taylor & Francis Ltd

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A Comparison of Non-Bonded Scaling Approaches for Free Energy Calculations

By Pitera Jed W.   van Gunsteren Wilfred F.  

Molecular Simulation, Vol. 28, Iss. 1, 2002-01 ,pp. : 45-65

Taylor & Francis Ltd

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Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations

By Lavery R.  

Nucleic Acids Research, Vol. 31, Iss. 5, 2003-03 ,pp. : 1434-1443

Oxford University Press

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Free Energy Simulations Over Creation/Annihilation Paths for a Flexible Solute

By Mezei Mihaly  

Molecular Simulation, Vol. 28, Iss. 1, 2002-01 ,pp. : 39-44

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