SARvision | CDDVault | Biologics | Sequence Analysis

Analyzing Sequences from CDDVault

by Mark Hansen, Ph.D.

 

SARvision works seamlessly with CDDVault to study both small molecules and biologics such as peptides and antibodies. Sequences and pharmacological data can be stored and then analyzed using SARvision|Biologics in the same way small molecules are studied in SARvision|Small Molecule. SARvision can access CDDVault using any available saved search to retrieve data. To get started, credentials to login must be generated on the CDDVault website. These credentials will be required only the first time and will be encrypted locally and remembered by the program for subsequent data requests. To obtain a credential token, log onto CDDVault, go to Settings, select API Keys and add a new key. Copy this key for use in SARvision in the next steps below.

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To import data into SARvision, go under the main menu and select File->Import from->CDDVault to open the CDDVault import dialogue. SARvision|Biologics is shown as an example, but the Small Molecule version behaves similarly. The first time an API token (obtained as described above) must be entered on the top text box. This key acts as credentials to access CDDVault. In SARvision, preprogrammed searches in CDDVault can be prepared for easy access. These are listed in the dialogue in a list that can be selected for searching.

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Select import at the bottom to retrieve the relevant data from CDDVault for analysis in SARvision. Once the data has been loaded, different views, filters and scaffolds can be added to the view to facilitate analysis.  The project can be saved and then at a later date, data can be reloaded to capture the most current data.

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The Monomer table (and the modifier table if used) can be loaded automatically from CDDVault as well. Under main menu->Tools->Resource manager the CDDVault connectivity to load monomers can be set up similarly to loading sequences. In CDDVault, a separate vault should be created to store monomer structures and the data-fields in a format consistent with the monomer table (See getting started for formats). Once set up monomers will be automatically loaded from CDDVault as necessary. CDDVault can take care of maintaining a consistent monomer library across multiple researchers and/or research groups.

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**Note that once a project has been set up in SARvision, it can be saved as a project file (*.svsm or *.svb). This can be opened at a later date or shared or opened by another user. Clicking on the reload button will go back to the sources, including CDDVault, and reload a fresh set of data. To reload data, the user opening the file must have created an API token and the Vault data to access CDDVault: the token is not saved with the file. Creating project this way is an easy way to distribute analyses across teams so that they can look at the same data that is up to date with the corporate repository.

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Working with Subsets

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How to Prepare Monomer Tables for Biologics Research