Computational techniques designed to predict the spatial structure of ligand-receptor complexes (molecular docking) are widely used in investigations of molecular details of protein functioning and in drug design. Here, a brief review of docking methods is given and recent advances in improvement of their accuracy and efficiency are discussed. Two acute problems of standard docking algorithms are considered: proper ranking of putative docking solutions and simulation of receptor flexibility. The recent trends to overcome these problems are demonstrated with the results obtained in our Laboratory. Particular attention is paid to protein-ligand hydrophobic and stacking interactions, which are not always adequately represented in scoring criteria of docking applications. © 2009 Springer Netherlands.