Valdés-Tresanco, M.S.; Valdés-Tresanco, M.E.; Jiménez-Gutiérrez, D.E.; Moreno, E. Structural Modeling of Nanobodies: A Benchmark of State-of-the-Art Artificial Intelligence Programs. Molecules2023, 28, 3991.
Valdés-Tresanco, M.S.; Valdés-Tresanco, M.E.; Jiménez-Gutiérrez, D.E.; Moreno, E. Structural Modeling of Nanobodies: A Benchmark of State-of-the-Art Artificial Intelligence Programs. Molecules 2023, 28, 3991.
Valdés-Tresanco, M.S.; Valdés-Tresanco, M.E.; Jiménez-Gutiérrez, D.E.; Moreno, E. Structural Modeling of Nanobodies: A Benchmark of State-of-the-Art Artificial Intelligence Programs. Molecules2023, 28, 3991.
Valdés-Tresanco, M.S.; Valdés-Tresanco, M.E.; Jiménez-Gutiérrez, D.E.; Moreno, E. Structural Modeling of Nanobodies: A Benchmark of State-of-the-Art Artificial Intelligence Programs. Molecules 2023, 28, 3991.
Abstract
The number of applications for nanobodies is steadily expanding, positioning these molecules as fast-growing biologic products in the biotechnology market. Several of their applications require protein engineering, which in turn would greatly benefit from having a reliable structural model of the nanobody of interest. However, as with antibodies, structural modeling of nanobodies is still a challenge. With the rise of artificial intelligence (AI), several methods have been developed in recent years that attempt to solve the problem of protein modeling. In this study, we have compared the performance in nanobody modeling of several state-of-the-art AI-based programs, either designed for general protein modeling, such as AlphaFold2, OmegaFold, ESMFold and Yang-Server, or specifically designed for antibody modeling, such as IgFold, and Nanonet. While all these programs performed rather well in constructing the nanobody framework and CDRs 1 and 2, modeling of CDR3 sill represents a big challenge. Interestingly, tailoring an AI method for antibody modeling does not necessarily translate into better results for nanobodies.
Keywords
artificial intelligence; protein structure; protein modeling; nanobody; antibody
Subject
Biology and Life Sciences, Biochemistry and Molecular Biology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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