Computational approaches to the identification of heparin-binding sites on the surfaces of proteins

The identification of heparin-binding sites is important for understanding the physiological function of many secreted proteins. Most of the experimental techniques for mapping these sites do not define them to atomic resolution. The use of automated docking methods can aid this process by facilitating both the design of experiments and visualization of their results. A method designed for a systematic search over the whole protein surface for heparin-binding sites, using heparin oligosaccharide structures as ligands, is described, with its validation and details of several published applications. The scope and limitations of this crude but effective computational chemistry method are discussed.