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Curated and Ready-to-use Protein Models with Orion® MMDS

Orion® MacroMolecular Data Service

In drug discovery, quality of structural data is key to understanding modeling results. Preparing proteins from experimental data for structure-based discovery contains many critical steps.1 In the Orion® MacroMolecular Data Service (MMDS), we have simplified the process for you.

With Orion MMDS, you have access to more than 38,000 pharmaceutically relevant protein structures, classified by functions,2 annotated for model quality,3 and readily prepared for your modeling needs. You also can prepare and upload* protein structures from your own in-house collection.

  •
    In Orion MMDS, family trees can be used to sort projects with similar structure so they can be superposed and compared in 3D. Here, an HIV protease structure is loaded into a BACE1 project for comparison as both structures are from the aspartyl protease family.
  • Rapidly assess the quality of different protein crystal structures with Iridium scoring. In Orion MMDS, proteins of similar structure are sorted in a way that allows them to be superposed and compared in the 3D visualizer. Selecting Highly Trustworthy (HT) ranked structures provides you a higher confidence for your virtual screening needs.
  • In Orion MMDS, choose your model's style, coloring, labeling, and water & H-bond preferences to visualize your protein-ligand complexes of interest.

Fast Structure Loading and List Curation

Directly access >38,000 highly curated protein structures. Or load your structures directly using pre-built workflows in Orion*

  • Input data from the PDB or from internal lists.
  • Upload just the protein/target or include additional components, such as ligand and solvent.
  • Tag data to identify experiments, sites, contexts.
  • Arrange structures by family and sub-family.
  • Curate and share structure lists with internal users.
  • Easily add, remove, or rearrange structures within project lists.
  • Use pre-built Orion Floes or create your own customized session.

Reliable Scoring and Assessment

Prepare, score, and assess protein structures using trusted OpenEye science.

  • Choose whether to analyze just your protein/target or include additional components, such as ligand and solvent.
  • Assess model quality using Iridium criteria.3
  • Integrate the proteins or ligands for use in OpenEye’s Gigadock™ functionality and through FastROCS shape.
  • Perform similarity searching within the Orion platform.

Customizable 3D Viewing and Comparison

Customize your 3D-model view so you can work intuitively and quickly.

  • Choose your model's style, coloring, labeling, and water & H-bond preferences.
  • Select the mouse-mapping option that works best for you.
  • Search for similar structures and superpose 3D models for quick comparison.
  • Compare protein sequences and highlight backbone deviations.

* Available with the Orion’s optional Managed Stack platform choice.

References:

  1. Grebner C, Norrby M, Enström J, Nilsson I, Hogner A, Henriksson J, Westin J, Faramarzi F, Werner P, Boström J. 3D-Lab: a collaborative web-based platform for molecular modeling. Future Med Chem. 2016 Sep;8(14):1739-52. doi: 10.4155/fmc-2016-0081. Epub 2016 Aug 31. PMID: 27577860. 
  2. IUPHAR/BPS Guide to Pharmacology 
  3. Warren GL, Do TD, Kelley BP, Nicholls A, Warren SD. Essential considerations for using protein-ligand structures in drug discovery. Drug Discov Today. 2012 Dec;17(23-24):1270-81. doi: 10.1016/j.drudis.2012.06.011. Epub 2012 Jun 21. PMID: 22728777. 

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