2019.2.1 Release

OpenEye is pleased to announce the first release of Orion, a cloud-based, cloud-native modeling platform for computer-aided drug design. Orion’s elements reside on Amazon Web Services (AWS), the world’s largest on-demand computing facility.

Orion uses AWS to deliver easy, scalable, maintenance-free access to hundreds, thousands, or even tens of thousands of processors as well as unlimited storage and archiving via reliable networks, all backed up by world-class data security. Orion can be accessed either directly through the customer’s relationship with AWS or indirectly through OpenEye.

Orion is an open platform that allows for straightforward integration of third-party code (i.e., from customers, academics, and vendors). The Orion front end is a webpage, deliverable on any internet-enabled supported platform.

Supported Browsers

  • Orion supports the most recent stable desktop versions of Mozilla® Firefox® and Google Chrome™.

Hint

Microsoft Internet Explorer (IE), Microsoft Edge, and macOS Safari are not supported.

Supported Platforms

  • Windows
  • macOS
  • Linux
  • Chrome OS

General

  • Orion organization admins can view user spending by project and user.
  • Orion organization admins can see all projects and jobs from all users.
  • Orion organization admins can only see project names but not the data in the projects.
  • Non-admins can only see their own projects and the projects shared with them.

Home

  • On Orion’s home page, users can view information about:

    • projects
    • recent jobs
    • system status
    • expenses
    • RSS feeds
    • A new user’s default project is created when the new user is added to the system.
    • Non-admin users’ projects are listed on an admin user’s Home page.
    • Duplicate project names are not allowed

Project Summary

  • Each project has its own Summary page. From the Project Summary page, users can:

    • edit or delete projects
    • add notes, molecular structures, and files
    • add or remove project members

Project Data

  • Users’ datasets, collections, and files are displayed on the Project data page.
  • Files can be uploaded to the Project Data page and converted to datasets, while datasets can be downloaded in the usual molecular formats.
  • Admin users can share files and datasets with the entire organization.
  • Collections can be filtered by name.
  • Datasets can be copied and/or duplicated.
  • Users can share multiple datasets to a project or with multiple recipients in one operation.
  • Users can add or remove data tags.
  • Datasets can be viewed using Card View.
  • Columns are sortable in Card View.
  • Individual molecules can be selected from the Card View to send to a Floe.

Analyze

  • The Analyze page’s features include:

    • a molecular spreadsheet
    • graphing capabilities—scatter plots, box plots, histograms, heatmaps, and violin plots
    • 2D and 3D viewing
    • molecule subset creation
    • filtering and tagging
    • cheminformatics functions—substructure search, R-group decomposition, and property calculation
  • Molecules can be sent directly to FastROCS from the Analyze page.

  • Molecules can be sent directly to a Floe using the Send to Workfloe feature.

  • Users can add comments and ratings for molecules in the Analyze page and the 3D Viewer.

  • Conformer data can be displayed in the spreadsheet and plot.

  • Receptors are by default designated as “3D Only” datasets, to keep them out of property calculations and the Analyze page.

  • Users can turn on binning on a per-column basis.

Floe UI

  • Users can upload packages containing Cubes and Floes.
  • Packages can be searched by name.
  • Floes can be shared with other users.
  • The Floe Editor allows users to build a new Floe or edit an existing Floe.
  • Users can place Cubes in a Cube group.
  • Cube groups can be deleted.
  • Running jobs can be monitored graphically.
  • Jobs can be filtered by project and user (admin-only functionality).
  • Parameters can be marked as “hidden” by the Floe author.
  • Initializer ports are colored blue to make them visually different from other port types.
  • Archive files (i.e., tar and zip files) are importable.

3D Viewer

  • The 3D Viewer includes functionality for perceiving protein and ligand interactions as well as for editing facilities for ligands in the context of the active site.
  • Users can convert molecules from 2D to 3D in the 3D Viewer.
  • Keyboard navigation can be used to cycle through conformers.
  • Users can send molecules from MMDS directly to the 3D Viewer.
  • Surfaces can be Z-clipped independently of other 3D objects.

Iterative Design

  • Iterative Design has functionality that allows users to generate new analogs of existing compounds. Users can edit molecules in 2D or 3D. Additionally, users can choose from the following algorithms:

    • Matched Molecular Pairs (MMP)
    • Near Fragment Replacement (NPR)
    • Reagent Join (RJ)
    • Explore Sidechains (ES)
  • Iterative Design and molecule builder tasks run on their own servers.

  • Property plots handle multiple pages of data.

  • If necessary, entry into an Iterative Design session can be cancelled by the user.

Data Sources

  • Two data services are available:

    • MacroMolecular Data Service (MMDS), a protein structure repository
    • FastROCS, a method for retrieving all similar structures by shape and color (aligned chemical groups) from a database
  • Users can send molecules directly to Orion from either data service.