The Good, The Bad, and The Ugly of Antibody Design: A Roadmap for Integrating Co-folding with Absolute Binding Free Energy Calculations
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Supporting data, structural models, and figure-generation scripts for: The Good, The Bad, and The Ugly of Antibody Design: A Roadmap for Integrating Co-folding with Absolute Binding Free Energy Calculations Amogh Sood*, Punit K. Jha*, Sheenam Khuttan, Dominic Rufa, Benjamin Shields, Alex Brueckner, Zane Beckwith, Andrea Bortolato, Mary Pitman. SandboxAQ, Palo Alto, CA, USA. (*equal contribution) Correspondence: mary.pitman@sandboxquantum.com Preprint / journal DOI: TBD This package accompanies the co-folding benchmarking portion of the paper for three antibody–antigen complexes — 1BJ1 (anti-VEGF Fab + VEGF, i.e. bevacizumab–VEGF-A), 3HFM (HyHEL-10 Fab + hen-egg lysozyme), and 1DQJ (HyHEL-63 Fab + hen-egg lysozyme) — plus an extended cross-tool structure-prediction campaign on 1BJ1. It contains every input, intermediate metric, and final figure used in the manuscript's structural-prediction sections. Data: CC-BY-4.0 Code (scripts): MIT How to cite: see CITATION.cff Companion code repository: the figure/analysis scripts are also published (code only, no structures) at https://github.com/sandbox-quantum/antibody-tango-publication.
