Docking sources

Check the outdoor air intakes to see whether they are located near contaminant sources (e.g., plumbing vents, exhaust outlets, dumpsters, loading docks, or other locations where vehicles idle). See if the space containing the HVAC system is clean and dry. Examples of problems include cleaning or other maintenance supplies... 

Alvarez JC. High-throughput docking as a source of novel drug leads. Curr Opin Chem Biol 2004 8 365-70. 

Figure 3.6 Docking simulations. (Source Liu H, Huang X, Shen J, et al. Inhibitory mode of 1,5-diarylpyrazole derivatives against cyclooxygenase-2 and cyclooxygenase-1 molecular docking and 3D QSAR analyses, Journal of Medicinal Chemistry 45 4816-4827 (2002). Used with permission.)...

Experimental information from biophysical or biochemical methods are the main source of data for the validation of the found docking poses. Thus, docking poses should not only be ranked according their score, but also according to knowledge obtained from experiments ... 

Furthermore, the models have to be reproducible. The model should give the same result when used by different users in different locations. This fact may lead to a preference toward easier models. Depending on the method for QS AR, some steps may be critical for reproducibility. Indeed, some approaches require manual optimization of the tridimensional structure of the chemical, e.g., in the case of tridimensional descriptors. In other cases, stochastic processes are used. Some more complex models done by skilled operators, such as docking, can be critical. Another source of variability is the software version or brand, even for simple bidimensional descriptors. 

YETI [198] is a force field designed for the accurate representation of nonbonded interactions. It is most often used for modeling interactions between biomolecules and small substrate molecules. The molecular geometry optimization for the component molecules is not previewed so that it has been obtained from some other source, such as AMBER. Then YETI is used to model the docking. 

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