FCCC    Clusters of Antibody CDR Loop Conformations     Dunbrack Lab

The Antibody Databases are updated monthly to reflect the most current PDB and can be downloaded from our download center via licensing.

Commercial licenses can be obtained by emailing Roland Dunbrack (Roland.Dunbrack@fccc.edu).

Database Name Description Usage
antibody_database_redundant.db CDRs and clusters for all identified antibody structures in the current PDB. Chains are from pdbaa on PISCES web site. It is the comprehensive database. The web site search is based on the redundant database.
antibody_database_nr_by_cdrs_per_chain.db CDRs and clusters for non-redundant by all 3 CDRs per chain. A chain must contains all three CDRs. The best chain in the same sequence group is selected in the order of: Lowest Resolution --> Lowest R factor --> Highest Chain Length. Mainly used for structure analysis and analysis of CDR/CDR interactions.
antibody_database_nr_by_cdr.db CDRs and clusters of non-redundant sequences for a given CDR type. IE All H1 are unique, all H2, etc. The CDR is selected in the order of: Lowest Resolution --> Lowest R factor --> Lowest normalized distance to the center structure. Mainly used for design and sequence analysis. Sequence logos are created using this database.
antibody_database_paper.db All identified, non-obsoleted CDRs from our original clustering paper It is used to build our CDR Hidden Markov Models (HMMs).
antibody_database_rosetta_design.db CDRs, clusters, structures and extra data used by the Rosetta antibody designer. The database is used for the Rosetta antibody design.