Release Notes¶

v0.1.11 July 2024¶

This package is built using OpenEye-orionplatform==6.1.2, OpenEye-toolkits==2024.1.1, and OpenEye-Snowball==0.28.0, OpenEye-orionmdcore==2.4.2.
The package is 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.
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.

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.