Author: Kuban-Jankowska, Alicja; Sahu, Kamlesh K; Niedzialkowski, Pawel; Gorska, Magdalena; Tuszynski, Jack A; Ossowski, Tadeusz; Wozniak, Michal
Title: Redox process is crucial for inhibitory properties of aurintricarboxylic acid against activity of YopH: virulence factor of Yersinia pestis Document date: 2015_7_22
ID: 1irvzt8v_30
Snippet: ΔG bind = ΔE MM + ΔG Polar + ΔG non−Polar ΔG Polar is the polar contribution to the solvation free energy and ΔG non−Polar is the non-polar contribution to the solvation free energy and is defined as ΔG non−Polar = γSASA + b , where γ = 0.0072 Kcal mol -1 Å -1 and b = 0 for AMBER-based GBSA calculations. SASA stands for the solvent accessible surface area. TΔS represents the entropic term and needs to be calculated by normal mode.....
Document: ΔG bind = ΔE MM + ΔG Polar + ΔG non−Polar ΔG Polar is the polar contribution to the solvation free energy and ΔG non−Polar is the non-polar contribution to the solvation free energy and is defined as ΔG non−Polar = γSASA + b , where γ = 0.0072 Kcal mol -1 Å -1 and b = 0 for AMBER-based GBSA calculations. SASA stands for the solvent accessible surface area. TΔS represents the entropic term and needs to be calculated by normal mode analysis, which is computationally expensive and since other ligands will bind to the same protein in the same binding site, we neglected the entropic contribution to the binding free energy in our calculations.
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