Virtual Screening Tool

High Throughput Docking as a Virtual Screening Tool... 

HIGH THROUGHPUT DOCKING AS A VIRTUAL SCREENING TOOL... 

Text-Mining as a Novel Virtual Screening Tool. 113... 

Fig. 4.1 Virtual screening tools can be categorized by the compound data to be screened (compound collection, combinatorial library, chemistry space) and the query type (structure-based, ligand-based, descriptor-based, pharmacophore-based). The output is always a list of compounds together with a score quantifying the fit to the query.

Virtual screening applications based on superposition or docking usually contain difficult-to-solve optimization problems with a mixed combinatorial and numerical flavor. The combinatorial aspect results from discrete models of conformational flexibility and molecular interactions. The numerical aspect results from describing the relative orientation of two objects, either two superimposed molecules or a ligand with respect to a protein in docking calculations. Problems of this kind are in most cases hard to solve optimally with reasonable compute resources. Sometimes, the combinatorial and the numerical part of such a problem can be separated and independently solved. For example, several virtual screening tools enumerate the conformational space of a molecule in order to address a major combinatorial part of the problem independently (see for example [199]). Alternatively, heuristic search techniques are used to tackle the problem as a whole. Some of them will be covered in this section. 

We have described two complementary tools for controlled modification of structures and their application to building databases for virtual screening. It is likely that virtual screening tools will integrate this capability to an increasing extent in the future. 

Validated QSAR Models as Virtual Screening Tools 445... 

Hawkins, P. C., Skillman, A. G., Nicholls, A. (2007) Comparison of shape-matching and docking as virtual screening tools. /Med Chem 50, 74-82. 

Assimilation of new data-mining and virtual screening tools into CDD for all users. 

Empirical Scoring, 264 2.4.3.S Knowledge-Based Scoring, 264 2.4.3.4 Consensus Scoring, 265 2.4.4 Docking as Virtual Screening Tool, 266 2.5 Filter Cascade, 267 3 Applications, 267... 

Figure 6.20. Flowchart of docking as virtual screening tool in the example of FlexX.

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