Calculate molecular properties
Using the Calculate Molecular Properties tool you can calculate commonly used properties of small molecules, such as Lipinski's rule of five or log P. These properties can be useful for identifying potential drug-like molecules, or for removing non drug-like molecules from a compound library before starting a large virtual screening experiment.
To run the "Calculate Molecular Properties" tool:
Toolbox | Drug Design (
) | Calculate Molecular Properties (
)
The Calculate Molecular Properties tool takes one or more Molecule Tables as input (figure 10.65).
Figure 10.65: Select Molecule Tables containing small molecules (ligands or docking results).
Note! Molecular properties will only be calculated for small molecules, i.e. ligands and docking results. All other molecules present in the tables will be ignored.
Click on the button labeled Next.
Figure 10.66: Molecular properties available in the Calculate Molecular Properties tool.
In the wizard step 2 (figure 10.66), the following molecular properties can be selected:
- Log P. The partition-coefficient log P is a measure of lipophilicity and is one of the criteria used to assess the druglikeness of a given molecule. The log P algorithm for a short description of the log P prediction algorithm used in CLC Drug Discovery Workbench.
- Lipinski's rule of five. Druglikeness of a given molecule is an important property. Lipinski formulated a simple set of rules that can be used to evaluate if a molecule has properties that would make it a likely orally active drug in humans[Lipinski et al., 2001]:
- Not more than 5 hydrogen bond donors (counted as the total number of nitrogen-hydrogen and oxygen-hydrogen bonds)
- Not more than 10 hydrogen bond acceptors (counted as the total number of nitrogen and oxygen atoms)
- Molecular weight
500 daltons
- Log P (octanol-water partition coefficient)
5
- Element counts. This option counts the number of H, C, N, O, P, and S atoms in the molecule. All other atoms are summarized in the 'Other atoms' column. These values can be useful if you are looking for the presence of a particular element or a certain composition of element types (the filtering can be done using the filter tool in the Molecule Table).
- Flexible bonds. This option reports the number of rotatable covalent bonds (single order, non-terminal bonds, which are not part of a ring system).
In the wizard step 3, choose to "Open" or "Save" the results and click on the button labeled Finish.
For each Molecule Table given as input, a corresponding Molecule Table containing calculated molecular properties is provided as output. The calculated molecular properties will appear as new column entries. The settings in the Side Panel can be used to toggle each property on or off (Show Columns palette). An example of calculated properties is shown in figure 10.67.
Note! The calculated molecular properties will overwrite existing information in the Molecule Tables if the column names are identical.
Figure 10.67: Ligand molecules with calculated molecular properties.
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