Release Notes

v0.1.8 July 2024

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.

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.

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.