Essential considerations for using protein-ligand structures in drug discovery.

By G. Warren, Thanh D. Do, B. Kelley, Anthony Nicholls, S. D. Warren. 2012

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SWEETLEAD: an In Silico Database of Approved Drugs, Regulated Chemicals, and Herbal Isolates for Computer-Aided Drug Discovery (2013, neutral): “correctness of the structural model[21].”
Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0] (2021, background): “The evaluation criteria deﬁned by OpenEye Iridium [70] can guide the assessment of X-ray structures.”
How accurately can one predict drug binding modes using AlphaFold models? (2023, background): “2 ligands bind is critical both to discovering early-stage drug candidates and to optimizing their properties (Maveyraud & Mourey, 2020; Warren et al., 2012).”
Best practices for constructing, preparing, and evaluating protein-ligand binding aﬃnity benchmarks [Article v0.2] (2021, background): “The evaluation criteria deﬁned by OpenEye Iridium [70] can guide the assessment of X-ray structures.”
Vinardo: A Scoring Function Based on Autodock Vina Improves Scoring, Docking, and Virtual Screening (2016, methodology): “The first dataset analyzed is Iridium-HT [16], which was also used in the final steps of Vinardo development (see Materials and Methods, section 4.1.2).”