Release Notes

v0.4.1 July 2024

General Notice

  • This package is built using OpenEye-orionplatform==6.1.2, OpenEye-toolkits==2024.1.1, and OpenEye-Snowball==0.28.0.

  • Updated to latest version of FPocket: fpocket==4.2

Floe Updates

  • The SiteHopper Search Floe has been optimized for faster searching and lower costs. These improvements result in a break in backwards compatibility with old SiteHopper Database Collections. New versions of SiteHopper MMDS Patch Collections (OEv2.0) have been created for searching. Any collections created prior to this release will not be compatible with SiteHopper Search. Results from this floe can utilize filters on Target Names.

  • The Make SiteHopper Patch Database Floe creates a SiteHopper Patch Collection that is compatible with the current SiteHopper Search Floe.

  • The DU to PDB floe now uses a design unit parameter so that a user can specify the input design unit on the record.

v0.3.9 February 2024

General Notice

  • This package is built using OpenEye-orionplatform==6.0.0, OpenEye-toolkits==2023.2.3, and OpenEye-Snowball==0.27.0.

Floe Updates

  • The Enumerate Pockets on Design Units Floe will now include pocket enumeration using the f-pocket method. The f-pocket method is turned on by default using established minimum and maximum pocket size parameters.

  • The Mutate Residue(s) Floe now uses the latest Omega toolkit to generate mutant conformers, and may result in very small differences in R-group placement

  • The DU to PDB Floe now respects output path

v0.3.8 July 2023

General Notice

  • This package is built using OpenEye-orionplatform==5.1.0, OpenEye-toolkits==2023.1.0, and OpenEye-Snowball==0.26.0.

Floe Updates

  • A new Floe, Protein Loop Modeling or Remodeling, has been added. This Floe will build missing loops or will rebuild a loop on a protein. Inputs must indicate where on the protein the loop is to be attached and the sequence that is to be built. The conformers with lower energies will be favored.

  • Descriptions have been improved to clarify inputs and how a change is going to affect the DU.

v0.3.6 December 2022

General Notice

  • This package is built using OpenEye-orionplatform==4.5.3, OpenEye-toolkits==2022.2.1, and OpenEye-Snowball==0.25.1.

Floe Updates

  • The Make SiteHopper Patch Database floe is now able to incorporate a Target Name into the built SiteHopper databases if UniProtKB data is provided. If a database is built with target information, it will persist in the hitlist search result when the database is screened. New databases will be deployed with this release that has target information incorporated.

  • A new floe DU to PDB has been added. The floe converts design units on datasets to PDB files and places them in the Exports/ folder in a users My Data directory.

  • A new floe Subset Design Unit to Smallest Binding Unit has been added. This can reduce design units on datasets to the smallest unit relating to a binding site, e.g. a dimer system can be reduced to a monomeric system if the binding site is situated in a single chain. This can be helpful to reduce the time and cost of certain types of calculations that scale with system size, with the assumption that the other parts of the system (the other monomer in the case above) are not needed to understand the property being investigated.

v0.3.5 September 2022

General Notice

  • This package is built using OpenEye-orionplatform==4.4.0, OpenEye-toolkits==2022.1.1, and OpenEye-Snowball==0.24.1.

Floe Updates

  • When making a sitehopper search database, the floe now more cleanly handles large records that fail to produce a DU for processing.

  • When doing a sitehopper search, only allow for a single record to be passed into subsequent searches. Description also changed to make this more clear.

v0.3.2 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.

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

Floe Updates

  • The DU to Mol floe has been improved to properly set a primary molecule on the output record, making it easier to use this floe before exporting to a PDB file.

  • The SiteHopper Patch Database generation floe now properly stores the target name if provided on the input data records or shards.

  • The SiteHopper Search floe will now again put PDB code and DU title in the search results. The target name will also be available if it was stored in the SiteHopper Patch Database.

  • The SiteHopper Patch Database Generation and Search floes have been updated to make it possible to send a dataset or record directly to the floes as input in the Orion user interface.

  • The failure reports in all floes have been improved to properly log the title of the design unit on a record in question.

v0.3.1 December 2021

General Notice

  • This package is built using OpenEye-toolkits==2021.2.0, OpenEye-orionplatform==4.2.5, and OpenEye-Snowball==0.23.1.

  • The MMDS floes have been moved to a separate dedicated package.

Floe Updates

  • The SiteHopper floes have been re-worked due to the OpenEye toolkit release of SiteHopper.

  • The SiteHopper database building floe can now accept spruce prepared datasets, in addition to the former MMDS prepared collections. There is now also an option to build a database of alternate sites on the input protein structures, using both OEPocket and F-pocket to enumerate sites on the protein structures.

  • There is now a stand-alone floe to find alternative binding sites on design units.

  • The modeling floes, sidechain builder, capping, mutation, updating components, now have an optional path to add explicit hydrogen and partial charges, making their use in downstream floes straightforward.

Data Updates

  • With this package we are also deploying two pre-built SiteHopper databases, based on prepared design units of structures for targets in the Guide to Pharmacology database. One collection is of ligand binding sites, or known ligand binding sites, whereas the other is of potential binding sites, where sites have been enumerated with OEPocket and F-pocket. The liganded-collection is around 40,000 patches, whereas the potential site collection is around 300,000 patches, in addition it is worth noting in terms of search time, that the potential sites are generally larger and more variable in size, increasing the search time for SiteHopper. These collections are distributed in Organization data and the SiteHopper Collections folder.

Documentation Updates

v0.2.1 June 2021

General Notice

  • This package is built using OpenEye-Snowball==0.21.0 and the associated OpenEye-orionplatform

Floe Updates

  • Modified the DU to Mol Floe to use a modified converter cube to give users more control and the ability to output additional mol components into separate fields.

  • Updated the MMDS admin floes that make PDB Collection floes to use PDB files instead of service downloads.

Documentation Updates

v0.2.0 November 2020

General Notice

  • This package is built using OpenEye-Snowball==0.20.0 and the associated OpenEye-orionplatform

Documentation Updates

A tutorial, Search for Similar Binding Sites with SiteHopper, has been added, which guides the use of the SiteHopper Search Floe.

Floe Updates

A number of floes to support collecting, preparing and uploading prepared data into The MacroMolecule Data Service (MMDS) have been added. Most of these floes should ONLY be run by an MMDS administrator due to the permissions needed to add data to MMDS, as well as the cost associated with running these floes. The floes are divided into two sections. Data preparation 1-5 and Data upload 6-10. Dataset preparation floes 1 and 2 have specializations depending on the data source, being RCSB for PDB structures, or an in-house Proasis server product. The RCSB is a subset of the data and is organized by the family and target classification provided by Guide To Pharmacology

  • [MMDS ADMIN] MMDS 1. Make/Update RCSB PDB Collection: A Floe to store a collection of the experimental data, 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.

  • [MMDS ADMIN] MMDS 2. Generate Guide to Pharmacology Datasets: A Floe to pull and build a target and target family tree based on Guide to Pharmacology’s database.

  • [MMDS ADMIN] MMDS 3. Target Reference Picker: A Floe to generate a reference structure for a target based on consensus biological unit form and binding site location of all the structures in the target.

  • [MMDS ADMIN] MMDS 3b. Update target dataset: A Floe to update targets with new structures added since it was last run.

  • [MMDS ADMIN] MMDS 4. Family reference picker: A Floe to generate a reference structure at the family level nodes if all the child targets are superposable.

  • [MMDS ADMIN] MMDS 5. Structure Prep: A Floe to prepare all the structures stored in the PDB collection on a per target basis.

  • [MMDS ADMIN] MMDS 6. Add family data to MMDS: A Floe to upload the family dataset into MMDS.

  • [MMDS ADMIN] MMDS 7. Add context data to MMDS: A Floe to upload a context (target) dataset into MMDS.

  • [MMDS ADMIN] MMDS 8. Add structures to MMDS: A Floe to upload the prepared structures into MMDS.

  • [MMDS ADMIN] MMDS 9. Add receptors to MMDS: A Floe to pull and generate OEDocking receptors for each frame stored in MMDS

  • [MMDS ADMIN] MMDS 10. Add sequence alignments to MMDS: A Floe to pull and generate a sequence alignment for each target in MMDS.

  • [MMDS ADMIN] MMDS 11. 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.

  • [MMDS ADMIN] MMDS 1. Make/Update Proasis PDB Collection: A Floe, which is a specialized version of [MMDS ADMIN] MMDS 1. Make/Update RCSB PDB Collection meant for customers that have an in-house Proasis server that stores their structural biology data.

  • [MMDS ADMIN] MMDS 2. Generate Proasis Datasets: A Floe, which is a specialized version of [MMDS ADMIN] MMDS 2. Generate Guide to Pharmacology Datasets meant for customers that have an in-house Proasis server that stores their structural biology data.

Floes have been added to enable SiteHopper. The floes rely on input data sources produced by the MMDS data collection and preparation floes.

  • Make SiteHopper Patch Database: A Floe that takes a collection of prepared design units, and then generates a collection of patches for those structures.

  • SiteHopper Search: A Floe that takes a prepared OEDesignUnit record as the query and searches a provided patch database using the GPU. The results can then be refined via a CPU SiteHopper overlay calculation.

v0.1.1 August 2020

General Notice

  • Upgraded to use OpenEye-Snowball==0.19.0 and the associated OpenEye-orionplatform

Floe Updates

  • Updated floe names Subset DesignUnit and Subset Within DesignUnit to both include DesignUnit.

  • Update DU Content: A Floe to update the content of an OEDesignUnit

v0.1.0 April 2020

General Notice

  • This is the first release of Biomodeling Floes.

  • The package uses OpenEye-Snowball and the associated OpenEye-orionplatform.

The packages contains the following floes, which are considered bite-size examples of what can be done in biomolecular modeling.

  • Extract Biological Units: A Floe to extract biological units from asymmetric units.

  • Build Sidechains: A Floe to build out missing or partial sidechains in proteins.

  • Mutate Residue(s): A Floe to mutate protein residues in design units.

  • Residue State Changer: A Floe to change the state of a titratable residue in design units.

  • Rotamers of a Residue: A Floe to be able to get rotamers of a specified residue in design units.

  • Cap Chain Breaks: A Floe to cap protein chains breaks in design units.

  • Swap Metal(s): A Floe to swap metals in design units (e.g. to change crystallization metals with biologically known metals).

  • Minimize DU: A Floe to minimize components of in design units.

  • Superpose DUs: A Floe to superpose design units to a reference design unit.

  • Subset: A Floe to be able to remove undesired components of design units (e.g. excipients) before modeling.

  • Subset Within: A Floe to be able to subset e.g. solvent in design units to within 5A of the protein and ligand.

  • DU to Mol: A Floe to be able to convert design units to molecules for use in subsequent cubes and floes.

  • DU 2 Receptor: A Floe to be able to convert design units to docking receptors for use in subsequent cubes and floes.