The objective of molecular docking is the prediction of binding between two
molecules, given their three dimensional structures. There are two main tasks
in docking: the search for ways to make a complex and the scoring of such
complexes. The search methods can be divided in three main areas: systematic,
stochastic and simulation methods. The two critical elements in a search
procedure are speed and effectiveness in covering the relevant conformational
space. The scoring function should be fast enough to allow its application to a
large number of potential solutions and, in principle, effectively discriminate between
native and non-native docked conformations. The scoring function is also divided
in three main categories: those based on force fields used for energy calculation
of the system, empirical functions and knowledge-based functions. The scoring
function should include and appropriately weigh all the energetic ingredients.
To solve the docking problem, ideally, the best matching algorithms and scoring
schemes should be combined (Kitchen et al. 2004).
Successful docking requires an understanding of the macromolecular interactions
in question, in this case, protein-carbohydrate interactions. Protein binding sites for
small ligands and binding sites for glycans are different. The binding sites of small
ligands are often narrow cavities in which the small ligands will dock tightly. On the other
hand, binding sites for glycans are shallow groves. Carbohydrates bind onto a binding
surface rather than into a binding cavity as seen in Figure 1 below.
