The ChemConnector Blog by Antony Williams

As a result of work we are doing over on ChemSpider regarding LASSO I have become increasingly interest in the world of protein docking.  A great review article was just released. I highly recommend it if this is an area of interest for you.

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

Current Pharmaceutical Analysis, Volume 4, Number 1, February 2008, ISSN: 1573-4129

Montserrat Vaqué, Anna Ardévol, Cinta Bladé, M. Josepa Salvadó, Mayte Blay, Juan Fernández-Larrea, Lluís Arola and Gerard Pujadas

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.