Release Notes

v0.1.1 July 2022

Floe Updates

  • Fixed an issue related to context queries when adding sequences to the structures

v0.1.0 July 2022

General Notice

  • This package is built using OpenEye-orionplatform==4.4.0, OpenEye-toolkits==2022.1.1, and OpenEye-Snowball==0.24.0.

  • This is the first deployment of this package since moving the MMDS floes out of biomodeler floes and into this dedicated MMDS Floes package.

  • All floes have edited titles, a new brief parameter and floe categories.

New Floes

  • MMDS 01. Make/Update PDB File Collection A Floe to store a collection of the experimental data from the RCSB, ie. PDB or MMCIF structure files, and MTZ files in a collection in Orion. The floe is designed to be run continually to pick up any changes in the data at the source. Optionally, the latest AlphaFold structures can be saved in the collection.

  • MMDS 02. Generate Target and Family Dataset A Floe to pull and build a protein target and target family tree based on the Guide to Pharmacology’s database. All other proteins found in the RCSB protein data bank are saved an Uncategorized family tree. Target alternates and structure of the Uncategorized tree uses protein sequence information from UniProt to determine similarity.

    Reference structures for targets are based on consensus design unit formation and binding site location of all the structures in the target. Reference structures for families are generated should a reference structure at the family level nodes superpose with all the child targets.

  • MMDS 3. Structure Prep: A Floe to prepare all the structures stored in the PDB collection on a per target basis.

  • MMDS 4. Add family data to MMDS: A Floe to upload the family dataset into MMDS.

  • MMDS 5. Add context data to MMDS: A Floe to upload a context (target) dataset into MMDS.

  • MMDS 6. Add structures to MMDS: A Floe to upload the prepared structures into MMDS.

  • MMDS 7. Add receptors to MMDS: A Floe to pull and generate OEDocking receptors for each frame stored in MMDS

  • MMDS 8. Add sequence alignments to MMDS: A Floe to pull and generate a sequence alignment for each target in MMDS.

  • MMDS 9. Delete Bad Structure by Code: A Floe to delete a structure by code in MMDS, the prepped structure collection, the target dataset, and the PDB Collection.