The SAR Table app provides schemes for property fields, which can be used to colour-code property values, as well as providing units and operational range. Schemes can be selected from a default list, or modified to suit.

Overview

Selecting schemes

Colour interpolation

Editing schemes

Summary

Overview


The SAR Table app provides features for assigning scaffold/substituent fragments, interconverting with constructed molecules, and auxiliary data such as ID codes and properties. A property datum consists of several parts, such as value, units, modifier and error. By default, property values are displayed on the main view in text form, e.g. 10.5 μM. A property field can be associated with a scheme, which provides information about the property, such as units, operational range, and colour coding.

Consider a selection inhibitors for the Trypanosoma brucei parasite from Journal of Medicinal Chemistry 55, 140-152 (2012) link:

Selecting schemes


By default the SAR Table app displays the structural components, along with their activity values, as ordinary text:

To apply a scheme, first open the field list, and double-tap on the TbNMT property:

Within the field editor dialog, press the Scheme button, which opens up a list of current available schemes:

The schemes shown include the default list. If you have modified schemes, or imported tables that have their own custom schemes, these will also be available to choose from. Select the HeatMap scheme with micro-molar units:

The scheme is now associated with the property. The field editor dialog shows a coloured strip that shows the operational range of the scheme (10000 μM to 0.0001 μM), the midpoint (1 μM), and the colour variation throughout the range.

Applying the change affects the display of the table:

Any resolvable property value is now displayed onto a coloured backdrop, which is a strong visual cue, allowing a large amount of property or activity data to be perceived rapidly.

Colour interpolation


A scheme defines a range of values, which have corresponding colour codes. Property values that lie within the range are assigned a colour by interpolation. Values that are outside of the range have their colour capped to the minimum or maximum setting.

There are three colour values for each scheme, which correspond to minimum, middle and maximum propery values. Providing three reference colours allows for tricolor schemes, such as the HeatMap (or "traffic light") palette that is often used to indicate biological activity: red for poor activity, yellow for moderate activity, and green for high activity.

For property values that indicate a specific numeric value, without conditional modifiers or errors, the display uses a single solid colour to annotate the value, which is shown in column A below:

For property values that include a standard error, the annotation is shown as a gradient, which gives an indication of the error boundaries, i.e. low = value-error, high = value+error. This is illustrated in column B above, for which each of the micromolar activity values have a large standard error.

Property values that have the greater/less than modifier, i.e. > or <, the colour range is computed by considering one of the boundaries to be the minimum or maximum value for the scheme. For example, a value of > 10 μM is displayed as a gradient between 10000 μM and 10 μM. Columns C and D above illustrate this.

Editing schemes


Schemes can be modified, rather than just picking from a predefined list. In the field editor dialog, press the Scheme button to bring up the list. Select the reference starting point, then press the Modify button:

The following properties can be configured:

  • Name: The display-name for the scheme. It does not need to be unique.
  • Units: The units for each of the property values, or blank if it is a unitless property (e.g. log units). When a fresh property is edited, the units will be filled out from the scheme as the default.
  • Transform-to-linear: In order to provide colour interpretation, a function is necessary to transform the value into a linear form. Units of concentration, such as μM activity values, have a linear response after applying the log function. Units such as pKi have already been transformed by the log function, and so no units-to-linear function is required.
  • Colour triplet: The tricolour scheme can be modified to suit. There are two special shortcut values: HeatMap and Doppler, which are provided for convenience. Specifying colours manually is done by entering hexadecimal colour codes separated by commas, e.g. FF0000,FFFF00,00FF00 is the explicit encoding for the red/yellow/green "heat map" scheme, while FF0000,FFFFFF,0000FF encodes the red/white/blue "doppler" scheme.
  • Low, Medium, High: Three property values must be provided, which correspond to the extremes and the midpoint. The low value matches the first colour, the medium value matches the second, and the high value matches the third. While the medium value is usually placed at the mid point, it can occur elsewhere in the range, in order to create a lopsided effect.

The range of activity values often needs to be updated to suit the study. The default micromolar schemes are calibrated so that 1 μM is considered a moderate activity response, and is represented in yellow. For the example of Trypanosoma brucei inhibitors, none of reported inhibitors are highly potent, and so all of the activities are coloured from red-to-yellow.

Adjusting the low/medium/high values to 10000/1000/1 μM results in full use of the tricolour range, making the trends easier to identify visually:

Summary


Using property schemes allows data to be visually represented by colour, which is an effective way to highlight trends. Property schemes can be selected from a default list, and modified as necessary to suit the distribution of the property values.

See Also


Introduction to SAR Table (iOS), SAR Table: Scaffold Matching