Experimental Affinity Inputs

Experimental affinity values of ligands are used to generate comparison plots and tables comparing experimental and predicted results for \(\Delta\Delta G\)s and \(\Delta G\)s in the Floe Reports. A number of other performance statistics are also reported in a table accompanying these plots, which can be used to evaluate the quality of predictions made by NES.

Experimental affinities of ligands can be provided via a dataset or via a plain-text file.

Experimental Affinity Provided by a Dataset

Affinity data can be read directly from the Ligand Input Dataset. You must, however, specify the column of the dataset that contains affinity data and, optionally, the error in the affinity data. The units of the affinity data must also be specified.

In the Experimental Affinities From Posed Ligands parameter group the aforementioned columns and units can be selected.

  1. Use the Experimental Affinity Field to select the column that contains experimental affinity values. It only displays the columns from the datasets that have been input into the Job Form thus far.

  2. Experimental Affinity Units displays a drop-down menu of units. Select the one in which the affinity values are to be read. If affinities are in \(IC_{50}\), \(K_{I}\), and so on, then select 'pM', 'nM', 'uM', 'mM' or 'M'. If affinities are in \(pIC_{50}\), \(pK_{I}\), and so on, then select log. If, however, affinities are in free energies, select kcal/mol or kJ/mol.

  3. Use the Affinity Uncertainty Field to select the column that contains the error associated with the experimental affinity values. If not present, error is assumed to be 0.0.

Experimental Affinity Provided by a Text File

Affinity data can also be provided via a text file using parameters in the Experimental Affinities From A Text File group.

  1. Provide the file to the Experimental Affinities File parameter. The file can be in either whitespace delimited or CSV format.

  2. If the file is in CSV format, choose , (comma) as the Delimiter from the drop-down menu. The default is whitespace(s).

  3. (Optional) Select the appropriate Experimental Affinity Units if the text file does not have any. This selection is applied to all entries (i.e., lines) in the file.

All lines in this file can have one of the two syntaxes.

  • Whitespace delimited format: [ligand] [affinity] [{optional} error] [{optional} units]

  • CSV format: [ligand], [affinity], [{optional} error], [{optional} units]

where

ligand = the molecule name
affinity = the experimental affinity
error = the error in the experimental affinity. When absent, it is assumed to be 0.0.
units = 'kcal/mol', 'kJ/mol', 'pM', 'nM', 'uM', 'mM', 'M', 'log'. When log is chosen, it is understood to mean \(pIC_{50}\), \(pK_{I}\), and so on.

The fields can be separated by contiguous whitespaces (including tabs) or by a single comma (,). This allows for the use of CSV files. The default delimiter is whitespace(s). If comma is to be used (i.e., CSV files), it must be selected as the delimiter.

Mixing syntaxes

Mixing the two kinds of syntaxes in a single file is not allowed. It will result in an error and the floe will fail.

As mentioned above, in the absence of units, a choice can be made from a drop-down menu. This choice is imposed on all affinity values.

Mixing units

It is also possible to mix affinity values with different units. This is useful when values from multiple rounds of rational design or different sources are combined and the experimental affinities are in different units. If some ligands do not have units while others do, the Units selected from the drop-down menu is imposed on the values with missing units.

Affinity Conversion Table

Conversion of experimental affinity to kcal/mol is printed in the Affinity Floe Report. The following formulas are used:

Input Affinity

Conversion to kcal/mol

\(x~\pm~\epsilon~kcal/mol\)

No conversion

\(x~\pm~\epsilon~kJ/mol\)

\(x/4.184~\pm~\epsilon/4.184\)
\(x~\pm~\epsilon~(M|mM|uM|nM|pM)\)

e.g., \(K_I\), \(K_D\), \(IC_{50}\)
Can be generalized to quantities for which a smaller
concentration value implies a higher affinity.
\(RT~ln~x~\pm~|RT\epsilon/x|\)

Input affinity \(x\) is converted to molar (M) before applying the conversion formula.
T is temperature. Default 300 K.
\(x~\pm~\epsilon~(log)\)

e.g., \(pK_I\), \(pK_D\), \(pIC_{50}\)
\(-RT~x/log_{10}e~\pm~|RT\epsilon/log_{10}e|\)

\(x\) is assumed to have been derived from concentration in molar (M),
i.e., \(x=-log_{10}(conc~in~M)\)