Custom Databases for Molecule Search

OpenEye, Cadence Molecular Sciences, provides several curated databases for use in Molecule Search. Customers can also develop their own custom databases to suit the specific needs of their organization. This page discusses the second option. The documentation for the Orion Molecule Search page includes a section on various database options.

Custom databases can be added to Molecule Search. This allows you to search using your own curated corporate or organizational databases.

Custom database preparation is a role-specific task. SaaS admins and modelers can select collections and specify memory for databases. Database preparation floes are available to facilitate this process. Standalone Search admins have access to abridged Floe and Data pages for floe administration and file management. Modelers can also create custom databases.

Note

For assistance in creating a custom database, SaaS and Standalone Search admins should first contact OpenEye Customer Support at support@eyesopen.com.

Managed Service stack admins and modelers can also use OCLI to create and load custom databases.

Molecule Search Database Preparation Floes – Beta

The Molecule Search Database Floes prepare custom databases for Molecule Search. The documentation for these floes is contained in the User Guide, rather than the Orion Workflows Guide.

The How-to Guide discusses the preparation of custom databases using the Automated Preparation for Molecule Search Databases Floe.

Custom Database Preparation

There are two ways to prepare custom databases. The first is to use the custom preparation floes from molecule files as discussed in the how-to guide. By default, the automated preparation floe produces a 2D and/or 3D database as the output.

Alternatively, you can click the “Create Database” button on the Databases Tab in the System page. This button will lead you to the list of collections that you have in your files. Select a collection to use as input, and it will be turned into a database.

After a database is prepared, it will appear automatically as a custom database option on the Databases Tab. At this point, the admin or modeler who created the database can load it for use in molecule searches. Admins are able to share custom databases with their organization.

Caution

It is highly recommended to unload large custom databases when not in use to avoid unnecessary charges.

Sharing Permissions for Databases

Custom databases can be shared with others in the same organization. The type of permissions that can be shared vary with the user role.

SaaS and Standalone Search admins may share custom databases with their organizations via a “Share with Organization” toggle in the UI. Sharing through the UI grants users “read-only” access; that is, those users cannot load, unload, or delete databases. While modelers may create custom databases, they cannot share them with their organization.

Managed Service admins and modelers can share additional permissions for their database with their organization using OCLI. In addition to read-only access, permission to load, unload, and delete databases can be shared with any other users using OCLI. Load/unload permissions can be given separately from delete permission.