Fig. 4
From: StreaMD: the toolkit for high-throughput molecular dynamics simulations
Correlation between docking scores or calculated MM-GBSA free energies with experimental affinities for three benchmark data sets. MM-GBSA free binding energies were calculated for different dielectric constants (1 or 4) and considering or ignoring the interaction entropy term (with or without IE). Only compounds satisfying chosen criteria (average RMSD ≤ 5 Å and standard deviation of RMSD ≤ 0.5 Å) were used to calculate correlations. Scatterplots between docking scores or calculated free energies and experimental pKd values are available in Figures S2-S7. Correlation statistics for other trajectory segments and for all compounds is in Figure S9