Release Notes

v0.1.6 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 transformed into a dataset with input sequences stored in fields ensuring paired sequences are stored in the same record.

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

• Antibody Experimental Structure Prep: Antibody design units 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 and analyzed given one or more complete antibody systems, each treated in its entirety in a separate simulation.

• Antibody Mutate Residue(s): User-specified single- or multi-point mutations are applied to antibody structure(s).

• 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 subdivided 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.