Derek Prediction Setup

The prediction setup options define what information is searched in the knowledge base to create predictions. There are default settings for the options, but you can change these settings to suit your own needs. Most options are shared between predictions for single structures and batch predictions.

This topic includes help on:

To open the Derek Prediction Setup:

  1. Select a structure in the Predictions pane then either:


When you have specified your options, click to run a prediction.

To open the Batch Prediction Setup:

  1. Select the structures or SDfile (refer to the Creating Batch Predictions topic for a complete list of what files you can select for batch predictions) in the Predictions pane then either:


When you have specified your options, click to run a prediction.

Knowledge Bases

Select one or more knowledge bases to predict against. All the knowledge bases that have been added to Derek Nexus are listed here. See the Managing Knowledge Bases topic in Nexus help for further details.

Icons indicate the status of knowledge bases:

A Lhasa or custom knowledge base that is locked and read-only.

A Lhasa knowledge base that is certified, locked and read-only.


You can change the following options to include or exclude the perception of tautomers and structural fragments, and matching alerts without rules:


Contains the overall species of mammal and bacterium, plus sub-species, to be used in or excluded from the prediction. You must select at least one species.


Contains the complete set of endpoints that can be used in or excluded from the prediction. The endpoints are arranged in a parent/child structure with parent endpoints suffixed with (ALL). You can select individual child endpoints but if you select a parent endpoint, all its child endpoints are also selected.

You can use the Select All and Deselect All buttons to help you make your choices.

Structure Properties

This section is only shown for single structure predictions. For each structure, Derek Nexus includes a calculated value for logP, logKp and molecular weight. If you have your own values, you can enter them here.

Note  Structure properties are not available for batch predictions.

To edit values, select the 'Overwrite' check box, then select the value and change it.

Report Configuration

This section is only shown for batch predictions. Refer to the Derek Batch Prediction Setup topic for help with these options.


Using Filters

You can find specific species and endpoints using the filter boxes. As you enter an expression into the filter box the corresponding list changes depending on the match. You can use wildcards (? for one letter and * for more than one letter) in these boxes. You can also collapse and expand each tree by using and , or collapse and expand a section in a tree by using and .

Creating and Applying Defaults

If you change any settings, you can save these as your 'user defaults', which you can then use for other predictions.

To save the settings, click Set As User Defaults.

In future predictions, you can use your user defaults or the system defaults.


How Derek Nexus Perceives Hydrogen

In accordance with the convention for drawing chemical structures, Derek Nexus automatically assumes that:

In printed and hand-written documents, the convention is to show hydrogen atoms attached to:

Note  If a hydrogen atom is not attached correctly to an oxygen, nitrogen or sulphur atom, a valency violation message is shown in the Problems pane and you cannot create a prediction.