Assessing docking predictions

Figure 5 A summary of the results of the CAPRI predictions submissions made by predictor groups. For each target offered for docking prediction since CAPRI started in 2001, bars represent the cumulative percentages of submitted models evaluated as high-, medium-, or acceptable quality. The remainder comprises incorrect models and models disqualified because of an excess of clashes or low-sequence identity. With targets T27 and T48-49, two possible modes of assembly had to be considered when assessing the models (see Figure 7). Detailed results of the assessment are reported in Refs. 63, 64, 105,162, and 163.

Finally, it is important to mention that even incorrect docking models may bring useful information, as many models that poorly recall the native residue-residue contacts nevertheless predict interface residues quite well (see Section Assessing Interface Predictions ). 

Virtual screening uses computational docking methods to assess which of a large database of compounds will fit into the unliganded structure of the target protein. Current protocols and methods can, with up to 80% success, predict the binding position and orientation of ligands that are known to bind... 

Park, J. and Harris, D. (2003) Construction and assessment of models of CYP2E1 predictions of metabolism from docking, molecular dynamics, and density functional calculations. J. Med. Chem. 46, 1645-1660. 

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 All complexes were unpublished before the submission deadline. 

Aloy, R, E. Querol, F. X. Aviles, and M. J. Sternberg. 2001. Automated structure-based prediction of functional sites in proteins Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J Mol Biol 311 395-408. 

Structures of protein complexes are the basis for understanding protein interactions. Many of fhese structures will have to be built by docking. CAPRI provides a forum for crifical assessment of docking methods. Methods making use of experimental or predicted interface information appear promising. 

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