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. Author manuscript; available in PMC: 2011 Feb 15.
Published in final edited form as: Proteins. 2010 Feb 15;78(3):671–680. doi: 10.1002/prot.22596

Table II.

Correlation coefficients between experimentally determined and calculated TS binding free energies.a

Base Triphosphate-TS Sum
MD62+ Mg2+ MD62+ Mg2+ MD62+ Mg2+
PDLD/S-LRA 0.84 0.86 0.46 0.41 0.93 0.91
LRA 0.82 0.79 0.24 0.14 0.50 0.44
a

The correlations between ΔGTSbind,obs and ΔGTSbind,calc for the base and the triphosphate part of the dNTP-TS, as well as the sum of their contributions, were obtained for the PDLD/S-LRA and the LRA method and for two different magnesium models (MD62+ and Mg2+). Note that the weak correlation for the sum of base and triphosphate-TS when using the LRA method is due to not using a dielectric constant during the calculations.