PartiDesign: A structure-sequence co-design paradigm for practical all-to-all biomolecules design

PartiDesign is a unified structure–sequence co-design model that jointly generates 3D structures and matching sequences or chemical identities, achieving the highest estimated successful-design throughput on most benchmarks.

• Why it matters: Efficient, controllable generation across proteins, nucleic acids, and small molecules is limited by difficulty coupling 3D structure design with sequence or chemical-identity design in chemically diverse settings.
• What they did: The method extends La-Proteina’s partially latent framework to proteins, nucleic acids, and small molecules, using fine-grained control over secondary structure, chemical bonding, and amino acid preferences. It was trained using 128 Huawei Ascend 910B accelerators with 64 GB memory each.
• The result: On de novo design benchmarks against specified targets, it achieved the top estimated throughput under adopted compute-budget protocols on most benchmarks, and configurable constraints supported cyclic peptide and antibody design. A web server and open-source code enable non-programmers to generate binding partners.

AI summary of the abstract · may contain errors · not medical advice · read the paper.