Science and Education Publishing American Journal of Modeling and Optimization 2333-1267 4 3 2016 12 1 Docking and Ligand Binding Affinity: Uses and Pitfalls 74 114 EN María J. R. Yunta Departamento de Química Orgánica I, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain AJMO2016432 10.12691/ajmo-4-3-2 2016 8 30 2016 10 14 2016 11 29 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.