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. 2005 Feb 1;33(2):725–733. doi: 10.1093/nar/gki195

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© The Author 2005. Published by Oxford University Press. All rights reserved

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Thermodynamic cycles used for the calculation of relative free energy of binding of netropsin and distamycin to the d(CGCGAAAAACGCG)·d(CGCGTTTTTCGCG) duplex. Net corresponds to the netropsin molecule with a net charge of +2 e parameterized with the force field 45A4. NetN corresponds to the same molecule but having a net charge of +1 e. The perturbation part of NetN (boxed atoms in Figure 1) is parameterized with force field 45B4 (non-charged version of the guanidinium group). Dist is the distamycin molecule. The abbreviations ‘solvent’ and ‘complex’ correspond to the ligand that is free in solution and to the one that is in complex with the DNA.