ArticleMolecules (Basel, Switzerland)2023
Structural Modeling of Nanobodies: A Benchmark of State-of-the-Art Artificial Intelligence Programs.
Article in Molecules (Basel, Switzerland), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Reimagining computational macromolecular modeling: AI-driven approaches.Biophysical journal · 2026Review
- Combining AI Structure Prediction and Integrative Modeling for Nanobody-Antigen Complexes.Journal of chemical information and modeling · 2026Article
- A Generative Neuro-Symbolic AI for Protein Sequence Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Rational Design and Characterization of a Mutated Nanobody for Specific Targeting of Heparan Sulfate.Antibodies (Basel, Switzerland) · 2026Article
- Deep mining of the human antibody repertoire identifies frequent and genetically diverse CDRH3 topologies targetable by vaccination.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A survey of downstream applications of evolutionary scale modeling protein language models.Quantitative biology (Beijing, China) · 2026Review
- Assessing structural prediction accuracy for nanobody-small molecule complexes.Protein engineering, design & selection : PEDS · 2026Article
- Investigations on genomic, topological and structural properties of diguanylate cyclases involved inCurrent research in structural biology · 2025Article
- Nanobodies: From Discovery to AI-Driven Design.Biology · 2025Review
- Unveiling the new chapter in nanobody engineering: advances in traditional construction and AI-driven optimization.Journal of nanobiotechnology · 2025Review
- Balancing speed and precision in protein folding: a comparison of AlphaFold2, ESMFold, and OmegaFold.Frontiers in genetics · 2025Article
- An integrative structural biology approach to identify the binding mode of a nanobody towards the pea ascorbate peroxidase.Computational and structural biotechnology journal · 2025Article
- NABP-BERT: NANOBODY®-antigen binding prediction based on bidirectional encoder representations from transformers (BERT) architecture.Briefings in bioinformatics · 2024Article
- Probing Functional Allosteric States and Conformational Ensembles of the Allosteric Protein Kinase States and Mutants: Atomistic Modeling and Comparative Analysis of AlphaFold2, OmegaFold, and AlphaFlow Approaches and Adaptations.The journal of physical chemistry. B · 2024Article
- Discovery of nanobodies: a comprehensive review of their applications and potential over the past five years.Journal of nanobiotechnology · 2024Review
- TEMPRO: nanobody melting temperature estimation model using protein embeddings.Scientific reports · 2024Article
- Article
- VHH CDR-H3 conformation is determined by VH germline usage.Communications biology · 2023Article
- Ultrasensitive Electrochemical Immunosensors Using Nanobodies as Biocompatible Sniffer Tools of Agricultural Contaminants and Human Disease Biomarkers.Micromachines · 2023Review
- Review
Corrections and comments
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Authors and funding
4 authors.
Funding
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, the 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 CDR3 still represents a big challenge. Interestingly, tailoring an AI method for antibody modeling does not necessarily translate into better results for nanobodies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.