A structure-informed dataset for Affinity and Developability engineering.
Introduction
Building upon the foundation of AbDesign 1.0, which provided a broad overview of CDR-H3 mutations across multiple complexes, AbDesign 2.0 introduces a high-resolution, exhaustive mutational landscape for engineering. While the previous version focused on a diverse set of antibodies with a specific focus on CDR-H3, shifts the focus toward a single, therapeutically significant complex: Pembrolizumab-PD1 (PDB 5GGS).
By moving from a broad survey to a deep-dive approach, AbDesign 2.0 allows researchers to precisely gauge the effects of mutations across all heavy chain CDRs and key framework positions. Crucially, this version closes the loop on antibody engineering by pairing binding data with a comprehensive suite of developability assessments, providing a multi-dimensional view of how sequence changes impact biophysical fitness.
What's New in AbDesign 2.0?
Exhaustive Mutational Mapping: Unlike the per-position mutants in version 1.0, which were extensive but not exhaustive, AbDesign 2.0 features a complete set of mutations for the most variable positions in the heavy chain CDRs (as judged by AbDiver) and critical framework regions. So there are no "missing mutants" (with exception of one position) allowing for head-to-head comparison of design approaches.
Integrated Developability Profiles: : For every variant that is produced in sufficient amounts, we have performed a full developability assessment. This includes stability, hydrophobicity, aggregation propensity, and polyreactivity.
Therapeutic Focus: All data is centered on the Pembrolizumab-PD1 complex, making it a premier resource for studying the optimization of checkpoint inhibitors.
576
unique point mutations exhaustively covering the heavy chain CDRs and key framework positions.
3,150
biophysical characterizations, providing a deep look into the fitness of each variant.
346
successfully produced antibodies with complete developability and affinity profiles
Comprehensive Characterizations
For the antibodies produced in sufficient amounts, AbDesign 2.0 provides the following experimental metrics:
Binding Affinity: Full kinetic profiles (KD, kon, and koff) to determine how mutations influence target recognition.
Stability (Tm): Thermal melting temperatures determined via nano-DSF to assess structural integrity.
Hydrophobicity: Normalized values providing insight into the surface properties and solubility.
Aggregation Propensity: Measured via AC-SINS to identify variants prone to self-association.
Polyreactivity: A total polyreactivity score based on binding propensity against a panel of four antigens: BVP, Ovoalbumin, dsDNA, and Heparin.
We make the AbDesign 2.0 DB free for non-commercial use by non-commercial entities. If you are a commercial entity and would like to employ the data in your activities, please get in touch with us.
Citing this work
There is no formal manuscript for AbDesign 2.0 yet. If you use this data in your research, please cite this website: