ArticleProtein science : a publication of the Protein Society2021
The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes.
Article in Protein science : a publication of the Protein Society, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 23 citations in OpenAlex.
- Article
- Combining computational modeling and experimental library screening to affinity-mature VEEV-neutralizing antibody F5.Protein science : a publication of the Protein Society · 2025Article
- An outlook on structural biology after AlphaFold: tools, limits and perspectives.FEBS open bio · 2025Review
- Addressing epistasis in the design of protein function.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Hallucination of closed repeat proteins containing central pockets.Nature structural & molecular biology · 2023Article
- Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens.Journal of chemical theory and computation · 2023Review
- Assessing and enhancing foldability in designed proteins.Protein science : a publication of the Protein Society · 2022Article
- High-throughput screening, next generation sequencing and machine learning: advanced methods in enzyme engineering.Chemical communications (Cambridge, England) · 2022Review
- What Have We Learned from Design of Function in Large Proteins?Biodesign research · 2022Review
- The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes.Protein science : a publication of the Protein Society · 2021Article
- Recent advances in de novo protein design: Principles, methods, and applications.The Journal of biological chemistryReview
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The functional sites of many protein families are dominated by diverse backbone regions that lack secondary structure (loops) but fold stably into their functionally competent state. Nevertheless, the design of structured loop regions from scratch, especially in functional sites, has met with great difficulty. We therefore developed an approach, called AbDesign, to exploit the natural modularity of many protein families and computationally assemble a large number of new backbones by combining naturally occurring modular fragments. This strategy yielded large, atomically accurate, and highly efficient proteins, including antibodies and enzymes exhibiting dozens of mutations from any natural protein. The combinatorial backbone-conformation space that can be accessed by AbDesign even for a modestly sized family of homologs may exceed the diversity in the entire PDB, providing the sub-Ångstrom level of control over the positioning of active-site groups that is necessary for obtaining highly active proteins. This manuscript describes how to implement the pipeline using code that is freely available at https://github.com/Fleishman-Lab/AbDesign_for_enzymes.
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Registered trials
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