Comparing protein–ligand docking programs is difficult

By Jason C. Cole, Christopher W. Murray, J. Willem M. Nissink, Richard D Taylor, Robin Taylor. 2005

335 citations recorded by the source corpus.

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Citations in the corpus

Using AutoDock for Ligand‐Receptor Docking (2008, background): “There have been several excellent publications that compare docking methods and scoring functions (Kontoyianni et al. 2004; Warren et al. 2006) and provide some cautions on how such comparisons should be carried out (Cole et al., 2005).”
Advances and Challenges in Protein-Ligand Docking (2010, background): “Finally, how to evaluate different docking programs and scoring functions is another active area [153–157].”
Assessing protein–ligand interaction scoring functions with the CASF-2013 benchmark (2018, background): “However, fair comparison of docking methods is very challenging because molecular docking is essentially a multiple-dimensional optimization process, during which many factors could matter 57,58 .”
Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, background): “For these reasons establishing a rigorous comparison of proteinligand docking programs is a daunting task, as it is difficult to draw conclusions of general applicability [59].”
EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization (2007, methodology): “To ensure unbiased benchmarks, 45 complexes used for the validation of EADock were taken from a previous study.”
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go (2008, unknown): “Fourth, as pointed out by Cole et al .”