eng Science and Education Publishing American Journal of Modeling and Optimization 2333-1267 2017-10-30 5 1 24 57 10.12691/ajmo-5-1-3 AJMO2017513 article María J. R. Yunta mjryun@ucm.es 1 Departamento de Química Orgánica I, Facultad de Química, Universidad Complutense, Madrid, Spain The effect of weak intermolecular interactions on the binding affinity between ligand-protein complexes plays an important role in stabilizing a ligand at the interface of a protein structure. In this review article, we will explore the different ways of taking into account these interactions, mainly intramolecular hydrogen bonds, in docking calculations. Their possible limitations and their suitable application domains are highlighted. Inspection of the outliers of this study probed very stimulating, as it provides opportunities and inspiration to medicinal chemists, being a reminder of the impact that minimal chemical modifications can have on biological activities. http://pubs.sciepub.com/ajmo/5/1/3/ajmo-5-1-3.pdf molecular modeling weak intermolecular interactions intramolecular hydrogen bonding binding affinity computer aided drug design