American Journal of Modeling and Optimization
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American Journal of Modeling and Optimization. 2016, 4(3), 74-114
DOI: 10.12691/ajmo-4-3-2
Open AccessReview Article

Docking and Ligand Binding Affinity: Uses and Pitfalls

María J. R. Yunta1,

1Departamento de Química Orgánica I, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain

Pub. Date: December 01, 2016

Cite this paper:
María J. R. Yunta. Docking and Ligand Binding Affinity: Uses and Pitfalls. American Journal of Modeling and Optimization. 2016; 4(3):74-114. doi: 10.12691/ajmo-4-3-2


In this review article, we will explore the foundations of different classes of docking and scoring functions, their possible limitations, and their suitable application domains. We also provide assessments of several scoring functions on weakly-interacting protein-ligand complexes, which will be useful information in computational fragment-based drug design or virtual screening.

molecular modeling docking binding affinity drug scoring computer aided drug design

Creative CommonsThis work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit


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