DOCK tool

Table 10.4 3. Common docking tools for virtual screening.

Schulz-Gasch T, Stahl M. Binding site characteristics in structure-based virtual screening evaluation of current docking tools. J Mol Model 2003 9 47-57. 

Difficulties in these approaches include that, according to literature [57-59] and the authors own experience, there is no general preference to one superior docking tool and scoring function that adequately works for different problems. Furthermore, it is an open question whether the detection of the best docking mode and the ranking of molecules require different scoring functions. 

Stahl, M. and Schulz-Gasch, T. Practical database screening with docking tools. In Small Molecule-Protein Interaction, Waldmann, H. and Koppitz, M. (Eds.). Springer-Verlag, Berlin and Heidelberg, 2003, 127-150. 

Binding site characteristics in structure-based virtual screening evaluation of current docking tools. 

Tietze, S., Apostolakis, J. (2007) GlamDock development and validation of a new docking tool on several thousand protein-ligand complexes. J Chem Inf Model 47, 1657-1672. 

In the validation study by Hawkins et al. (60), the shapematching method ROCS was compared to 7 well-known docking tools, in terms of their abilities to recover known ligands for 21 different protein targets. The comparative study showed that the 3D shape method (ROCS) performed at least the same as, and often better than, the docking tools studied. Their work indicated that shape-based virtual screening method could be both efficient (in terms of the computational speed) and effective (in terms of hit enrichment) in virtual screening projects. 

Improbability of docked binding mode. Fast docking tools cannot produce reasonable solutions for all compounds. Often even some high-scoring compounds are found to be docked to the outer surface of the protein. Computational filters help to detect such situations. 

An objective assessment of the available scoring functions is difficult because only very few functions have been tested on the same data sets or with the same docking tool. For... 

The preparation of the active site depends on the docking tools being used. This step involves the addition of hydrogen atoms avoiding atomic clashes assignment of appropriate protonation states of titrat-able residues and correct tautomers of histidine residues, and involvement of structural water molecules in the binding cavity. 

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