Release Notes

v0.1.8 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 ImmuneBuilder: ImmuneBuilder==1.2 that addresses an issue with final model selection.

  • An issue was fixed where unrealistic side chains would be created during optimization after structure generation.

  • An issue was fixed where only some atoms in a residue side-chain were shown as visible.

Floe Updates

  • Import Antibody FASTA Files: VH and VL sequence are detected during fasta parsing, and peptidic ligands are appropriately ignored.

  • A bug was fixed which addresses incorrect residue numbering on some structures.

v0.1.3 April 2024

General Notice

  • This is the first release of the 3D Antibody Modeling Floes package.

  • This package is built using OpenEye-orionplatform==6.1.2, OpenEye-toolkits==2023.2.3, and OpenEye-Snowball==0.27.1.

The package contains the following floes, whose purpose is to prepare and analyze antibody structures in 3D for antibody drug discovery.

  • Import Antibody FASTA Files: Input antibody FASTA files are added to a dataset that saves sequences to antibody fields.

  • Antibody Sequences to 3D Models: Antibody OEDesignUnits are generated from sequence data for downstream modeling and applications.

  • Antibody Experimental Structure Prep: Antibody OEDesignUnits are prepared for downstream modeling applications using SPRUCE by providing PDB codes or PDB/MMCIF files (and MTZ).

  • Antibody CDR Loop Ensemble Generation: Loop building is used on CDR regions of an antibody to generate an ensemble of CDR loops.

  • Antibody MD Simulations with Conformational Analysis: MD simulations are performed given one or more complete antibody systems as input, each to be treated in its entirety in a separate simulation.

  • Antibody Mutate Residue(s): Residues in antibody structures are mutated.

  • Antibody SiteHopper-based Clustering: Input antibody structures are clustered using SiteHopper patches at the CDR surface.

  • Antibody Structure Relaxation: Antibody complexes are minimized with options to keep various parts fixed or flexible.

  • Antibody Subset System: Antibody design units are subsetted using various selection criteria.

  • Antibody Surface Patch Generation: Antibody structures are analyzed for structure properties, hydrophobic patches, and charge patches.

  • Renumber and Restyle Antibody: Antibody structures are renumbered and restyled using the selected numbering scheme.