What is protein-ligand docking?
For most of the proteins known to date, their biological role is incompletely understood. Even proteins which participate in a well-understood biological process may have interaction partners or functions which are unrelated to that process. Moreover, vast numbers of “hypothetical” proteins have been discovered during the human genome sequence program, for which there is no information at all, apart from their amino acid sequence. Indeed, for any protein, scientists attempt to answer the questions: does the protein bind in vivo? If it does, what is the 3D-structure of the complex and how strong/weak are the protein-ligand interactions? Protein-ligand docking is a molecular modeling technique to predict the position and orientation (the 3D-structure) of a protein in relation to a ligand (another protein, DNA, drug, etc.). Docking methods are based on purely physical principles; even proteins of unknown function (or which have been studied relatively little) may be docked. The only prere
