Models, Data, and Scripts Underlying "Robustification of RosettaAntibody and Rosetta SnugDock"

This repository contains the models, data, and scripts underlying the publication "Robustification of RosettaAntibody and Rosetta SnugDock" by Jeliazkov et al. Brief descriptions of the individual compressed files follow.

• fkic_H3.zip/master_H3.zip contain the models underlying Figure 4A. The models are compared against their corresponding crystal structures and the backbone RMSD is calculated for the CDR H3 (residues 95-102, Chothia definition). Each zip file contains PDB-labeled directories with homology models in the base directory and loop models in the "models" subdirectory. The "master" zip used the standard H3 modeling approach in RosettaAntibody. The "fkic" directory used the standard method plus fragment insertion.
• fragment_comparison.zip contains the scripts and raw data for Figure 4B.
• fragments.tar.gz contains the fragments used to model the antibodies loops (Figure 4A) and for the comparison in Figure 4B. The traditional protein loop models and fragments in Figure 4B are published separately by Pan et al. [to do: update citation].
• grafting_results.zip contains the data and analysis code behind Figure 3.
• other_stray_code.zip contains the analysis code for Figures 1, 5, and the supplemental figures.
• snugdock_example.zip contains the raw data for Figure 5 which is also to be published separately by Zhou et al. [to do: update citation].