![]() Five transformations between the ligands involved a change of the net charge and we implemented and benchmarked a semi-analytic correction (Rocklin et al., J Chem Phys 139:184103, 2013) for artifacts caused by the periodic boundary conditions and Ewald summation. ![]() For a subset of 33 ligands, we calculated relative binding free energies with free-energy perturbation. Consensus scoring gave decent results with a Kendall’s τ of 0.26 ± 0.06 and a Spearman’s ρ of 0.41 ± 0.08. The selected docked poses gave an average root-mean-squared deviation of 4.2 Å. First, we employed docking with five different docking software and scoring functions. We have studied the binding of 102 ligands to the farnesoid X receptor within the D3R Grand Challenge 2016 blind-prediction competition.
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