Protein-ligand Docking: A Review of Recent Advances and Future Perspectives

Gerard      Pujadas; Montserrat      Vaque; Anna      Ardevol; Cinta      Blade; M.   Josepa   Salvado; Mayte      Blay; Juan      Fernandez-Larrea; Lluis      Arola

Abstract

Understanding the interactions between proteins and ligands is crucial for the pharmaceutical and functional food industries. The experimental structures of these protein/ligand complexes are usually obtained, under highly expert control, by time-consuming techniques such as X-ray crystallography or NMR. These techniques are therefore not suitable for routinely screening the possible interaction between one receptor and thousands of ligands. To overcome this limitation, computational algorithms (i.e. docking algorithms) have been developed that use the individual structures of the receptor and ligand to predict the structure of their complex. The present review, then, summarizes: (a) the fundamentals of the algorithms of the most commontly used docking programmes (with particular emphasis on their strengths and limitations); (b) how the results from different docking algorithms compare (i.e. which software gives the best predictions); and (c) the future perspectives and challenges for docking techniques.

Keywords: eHiTS, GOLD, Molegro Virtual Docker, AutoDock, Glide