Protein-ligand docking complexes

In CASP II (Critical Assessment of Methods of Protein Structure Prediction Round II), a new prediction section on protein-ligand docking was introduced [154]. Several groups participated and submitted up to three models for some of the seven protein-ligand complexes (see [155-158] for reports). For each target, the 3D structure of the protein and the 2D structure of the ligand was given to the participants. All complexes were unpublished before the submission deadline. 

Empirical Models. The use of empirical models is widespread in both academia and indnstry. There are for example a large number of statistical potential fnnctions that have been developed to address problems such as protein folding or protein-ligand docking. The appeal of snch models is that they can be designed to be compntationally inexpensive and can be fitted directly to experimental data to hopefnlly yield immediately meaningfnl resnlts for complex systems. The challenge is that systematic improvement of empirical models beyond a certain point is extremely difficult and becomes more difficnlt as the basis for the model becomes less physical. 

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