Docking and Ligand Binding Affinity: Uses and Pitfalls

eng Science and Education Publishing American Journal of Modeling and Optimization 2333-1267 2016-12-01 4 3 74 114 10.12691/ajmo-4-3-2 AJMO2016432 article Docking and Ligand Binding Affinity: Uses and Pitfalls María J. R. Yunta mjryun@ucm.es 1 Departamento de Química Orgánica I, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain 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. http://pubs.sciepub.com/ajmo/4/3/2/ajmo-4-3-2.pdf molecular modeling docking binding affinity drug scoring computer aided drug design