Heparin, a glycosaminoglycan (GAG), is a complex carbohydrate of varying chain length and consisting of uronic acid and glucosamine residues, which are sulfated at various positions.¹ Heparin and heparan sulphate (HS) oligosaccharides contain similar structural units in varying proportions, with different ring conformations providing considerable diversity in sequence and biological function. Heparin and HS play critical roles in a number of physiological and pathological processes such as inflammation, neural growth, angiogenesis, and viral invasion. These multifaceted roles arise from their interaction with a multitude of proteins. A potentially powerful approach to characterise heparin−protein interactions is molecular modelling. Nonetheless, modelling GAGs is complicated by their polyanionic nature and poor surface complementarity unlike small molecules. We present herein a molecular modelling approach aimed at characterising the molecular basis underlying the interactions of GAGs with heparanase² and CXCL-8.³ Heparin has been used to model compounds for the sulphated, protein-binding regions of HS despite the availability of a natural library of millions of GAG sequences. A virtual screening approach for predicting high specificity heparin / HS sequences towards chemokines is also presented.