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    May 10, 2024

    CDD Vault Update (May 2024): Overlay & Customize Dose-Response Plots, Bioisosteric Compound Suggestions, Parser Updates, and Quickly Search Related Protocols

    Hooray for curve overlays! We are excited to announce a new round of features associated with our Curve Analytics Module. If you are not yet subscribed to Curve Analytics, please contact your CDD Vault account manager or the CDD Vault Support Team to discuss enabling these features in your Vault.

    Curve Overlay

    Without leaving CDD Vault, you can now create a plot that displays curves of multiple molecules and/or curves with data from multiple protocols.

    Using the pop up window, add curves from different molecules and protocols. The new plot will open in a separate tab.

    Show/Hide Curves

    When multiple curves are displayed on a plot, you can choose which curves to show at any given time. Use the arrows above the compound structure (or keyboard) to navigate between curves and check the box at the bottom of the sidebar to hide a specific curve. You can also show/hide reference molecules.

    show hide curvesCustomize Appearance

    Adjust individual curves by changing the curve color, and size and shape of plotted points.

    Show/Hide Grid on Plot

    The settings gear icon in the top left hand corner of your plot will open up the plot settings panel on the right side of the page, allowing you to show or hide the grid lines on the plot.

    PDF Plot Exports

    After customizing your plots and obtaining the desired display, you can now export those plots as PDF files to be used in presentations or publications.

    CDD Vault’s Deep Learning features now include the option to generate compound suggestions with bioisosteric functional group replacements. If you do not have Deep Learning enabled in your vault, please contact your account manager or the CDD Vault Support Team to discuss enabling these features in your vault.

    Bioisostere Replacement Suggestions

    After navigating to a molecule’s overview page, click the link under the structure to “Suggest bioisosteres using deep learning similarity”. The pop up window contains molecule suggestions with structural replacements organized by attachment point. Calculate the chemical properties of the suggested structures on the fly with the gear icon. Then download the list of suggested structures to an excel file that includes the SMILES strings and calculated properties. Maybe you want to take a look at them in Visualization first before registering them in your vault?

    Bioisosteric suggestions can also be accessed in the search results table. The link displays underneath the structure and visibility is set in the Customize your Report interface.  

    Mining data across multiple protocols made simple!

    Protocol Data Search from the Protocol Index

    Using the filters on the Protocols subtab, you can narrow down your list of protocols. Clicking the “Explore Protocol Data” link will then launch a new query on the Explore Data tab that includes all data from the protocols displayed in your list. Easily retrieve data from multiple protocols with one click instead of building a search query with multiple terms.

    A previous feature release included the ability to create custom data parsers for data uploaded in a non-tabular format. These saved custom data parsers can be copied and imported for easy cross-vault sharing.

    Parser Index Page - Sharing

    After configuring a custom data parser, save it for later use. These saved parsers live on the Parsers subtab of the Import Data tab. They can be viewed, copied, downloaded, and deleted. After copying a parser, import that parser from your clipboard using the link in the upper right hand corner. For users who belong to multiple vaults, this is a quick and easy way to use the same custom parser in a different vault than the one it was created in.

    Parser - Replication of Plate Block and Auto-Adjusting Tabular Assignments

    Automation becomes easier when applying custom data parsers. The number of plates being used may vary from one experiment to the next. Now you can apply a custom data parser and repeat the assignments for any new data sections that have the same formatting. You can repeat the behavior on a single tab or across all tabs in your uploaded spreadsheet.

    This blog is authored by members of the CDD Vault community. CDD Vault is a hosted drug discovery informatics platform that securely manages both private and external biological and chemical data. It provides core functionality including chemical registrationdata visualization, inventory, and electronic lab notebook capabilities.

     

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