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Derek Nexus

DEREK NEXUS

Derek Nexus is the expert, knowledge-based software that gives you accurate toxicity predictions quickly. Early, accurate in silico toxicity tests using Derek Nexus is the quick, inexpensive way to identify potentially toxic chemicals, aiding your experts in rejecting unsuitable drug candidates.


Derek Nexus is the trusted expert toxicity system. It is based on data implemented by scientists at Lhasa Limited, who continually work on the toxicity knowledge base with current toxicological knowledge.

Benefits

How Derek Nexus Can Benefit You

Whether your industry is cosmetics, pharmaceuticals, chemicals, or you are in academia, Derek Nexus enables you to:

  • Evaluate the potential toxicity of existing or prospective chemicals.
  • Make decisions about which chemicals are likely to have ‘more favourable’ toxic profiles when you do not have all the experimental information you would like to have about the toxicity of each chemical.
  • Capture internal toxicity data and knowledge and make this information available to your colleagues.
  • Improve the properties of a chemical in the R&D pipeline by slightly redesigning its molecular structure.
  • Carry out toxicity experiments on a large number of chemical candidates where you could save time and money by selecting those with the most favourable outlook.
  • Act as a toxicology training or learning tool by using the extensive expert knowledge in the certified Lhasa knowledge base.

The certified Derek knowledge base, created and supplied by Lhasa Limited contains data from published sources and data donated by our member organisations. This data is collated, checked and verified by Lhasa scientists before being used to develop new knowledge rules and relationships. These rules and relationships are based on empirical observations that are supported by an understanding of the toxicity mechanism or by our internal rigorous vetting process.

Approach

How Derek Nexus Works

Using Nexus in the Lhasa Knowledge Suite, you submit your structures to Derek Nexus for processing. The structures are compared to the certified Lhasa knowledge base, or your own knowledge base that you have created using Derek Knowledge Editor, and a toxicity prediction is generated.

The Derek Nexus prediction includes an overall conclusion about the likelihood of toxicity in a structure and detailed reasoning information for the likelihood. The prediction is generated by applying expert knowledge rules in toxicology to the data returned from the knowledge base.

Endpoints

Derek Nexus predicts potential toxicity for most toxicological endpoints, including:

  • carcinogenicity
  • mutagenicity
  • genotoxicity
  • skin sensitisation (EC3 potency prediction) 
  • teratogenicity
  • irritation
  • respiratory sensitisation
  • reproductive toxicity

Derek Knowledge Editor

Derek Knowledge Editor enables you to create your own knowledge base that is based on the same schema used in the Lhasa-supplied Derek knowledge base.

This means that you can effectively capture your organisation’s knowledge from past research and make it useful and easily accessible to your current research programs. Using Derek Knowledge Editor, you can create and add knowledge, such as:

  • structure-activity relationships
  • knowledge rules
  • alerts
  • example structures
  • literature references
 

Derek Nexus Features

Derek Nexus has the following key features:

  • Fast processing — Derek Nexus has the ability to run one or multiple predictions quickly, including batch predictions.
  • Viewing patterns — You are able to view the patterns associated with the alerts that have fired for your query compound.
  • Powerful pattern language — Derek Nexus takes advantage of the schema and more powerful pattern language provided by the latest Derek Knowledge Editor.
  • Multiple knowledge bases — You can connect to, and process against, multiple knowledge bases simultaneously. This means that you can compare predictions from Lhasa knowledge and your own knowledge within seconds.
  • Multiple concurrent predictions — Multiple jobs can be run concurrently, including the ability to process single structures whilst also batch processing.
  • Easy prediction setup — There is one setup screen that enables you to set up the prediction to suit your needs.
  • Patterns in alert descriptions — Patterns are displayed in alert descriptions. This provides further transparency for alert matching.
  • Certified Lhasa knowledge base — Lhasa has certified its own knowledge so this cannot be edited. This confirms that the predictions are based on knowledge that has been implemented by Lhasa. Your own, custom knowledge can be stored in a separate knowledge base, which can be used to generate predictions simultaneously with the Lhasa knowledge.

Knowledge Editor Features

The main application of Derek Knowledge Editor is to create and edit knowledge bases that are used by Derek Nexus.

This release of Derek Knowledge Editor has the following key features.

  • Integrated Lhasa Limited structure editor — Enables you to enter pattern attributes and R-groups and removes the need to link to external, third-party structure editors.
  • Improved user interface — Functions are readily accessible, which makes the program user-friendly.
  • Search functions — You can run a detailed search for specific details of alerts, examples, patterns, reasoning rules, references, sources and toxicological data. A quick search for alerts is also available.
  • Online help and tutorials — Online help and tutorials are available from the Help menu. Some of the tutorials are also embedded in the online help.
  • Separation of entities — Enables you to view all aspects of the knowledge contained in the knowledge base in separate tables. For example, you can view patterns independently of alerts.
  • Multiple knowledge bases — Enables you to create, view and edit multiple knowledge bases from within the same interface.
  • Structure processing — Enables you to process a compound against all Derek patterns to find if it matches any of the inclusion patterns, or any of the on-path exclusion patterns. This allows you to assess whether a ‘Nothing to Report’ output from Derek Nexus is a near miss.
  • Preview pane — You can quickly assess the content of an alert through a preview pane.
  • Reusing entities — You can copy entities, for example, patterns, from the Lhasa knowledge base and paste them into your own, custom knowledge base. NOTE: You cannot edit any of the entities in the Lhasa knowledge base.
  • Alert and pattern testing — Enables you to test new custom alerts directly from within the editor rather than having to import the entire knowledge base in to Derek Nexus first. Additionally, you can test the matching of your pattern as you are creating it.
  • Powerful pattern features — Extensive enhancements have been implemented that enable you to express the following in a more detailed and/or efficient manner:
    • Atoms lists
    • Nested R-groups
    • R-groups with variable points of attachment
    • Logic operations for R-groups
  • Explora — Derek Knowledge Editor uses the Explora language, which is used to express complex attributes for atoms and bonds in patterns.

Web Services

Collectively referred to as the Derek Web Services, Lhasa Limited offers two web service solutions that can be incorporated into efficient internal processes by automating Derek Nexus into an institutional workflow.

The Derek Web Service

The service provides the user with a curated knowledge base and delivers results in a standardised (.xml) format. This gives users the flexibility to apply a front end that suits their needs for both pre- and postprocessing in your chosen system(s). For example, there may be the need to restrict selection of compounds to those stored within a central database, to store results in a project specific folder or utilise KNIME within your automated Derek workflow.

Derek Pipeline PilotTM Integration

In addition, we offer an integration option to provide the user with the relevant components with which to build a Pipeline Pilot protocol thereby exposing the curated knowledge from Derek Nexus, within Pipeline Pilot. The ability to standardise and automate processes can lead to more efficient working practices.

For more details on either solution, please refer to the brochure.

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