Provide a standard benchmark or test set for the prediction of protein-ligand binding affinities
We will collect and curate experimental for several test systems that allow us to assess the current state of affinity prediction computational methods (primarily free energy methods, though other approaches may be of interest) and learn about their current deficiencies. The curated experimental data will be posted on a publicly-accessible website, and practitioners will be encouraged to work on these systems. A publication will be produced describing the rational for their choice and the current challenges in pharmaceutical and biochemical research where free energy computation might be of high value.
Downloads
Curated datasets for a number of protein-ligand systems will be made available for download. These datasets will contain crystal and co-crystal structures, binding affinities collected from the literature, docked compound configurations, and references for all data sources. In addition, we will later offer molecular mechanics systems set up for major forcefields and simulation packages.
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