ArticleJournal of biological physics2020
ModiBodies: A computational method for modifying nanobodies in nanobody-antigen complexes to improve binding affinity and specificity.
Article in Journal of biological physics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 16 citations in OpenAlex.
- Assessing structural prediction accuracy for nanobody-small molecule complexes.Protein engineering, design & selection : PEDS · 2026Article
- Unveiling the new chapter in nanobody engineering: advances in traditional construction and AI-driven optimization.Journal of nanobiotechnology · 2025Review
- Molecular dynamics and machine learning stratify motion-dependent activity profiles of S-layer destabilizing nanobodies.PNAS nexus · 2024Article
- NABP-BERT: NANOBODY®-antigen binding prediction based on bidirectional encoder representations from transformers (BERT) architecture.Briefings in bioinformatics · 2024Article
- Structural Modeling of Nanobodies: A Benchmark of State-of-the-Art Artificial Intelligence Programs.Molecules (Basel, Switzerland) · 2023Article
- NbThermo: a new thermostability database for nanobodies.Database : the journal of biological databases and curation · 2023Article
- Dengue virus infection - a review of pathogenesis, vaccines, diagnosis and therapy.Virus research · 2023Review
- Modeling and affinity maturation of an anti-CD20 nanobody: a comprehensive in-silico investigation.Scientific reports · 2023Article
- INDI-integrated nanobody database for immunoinformatics.Nucleic acids research · 2022Article
- Engineered NK Cells Against Cancer and Their Potential Applications Beyond.Frontiers in immunology · 2022Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nanobodies are special derivatives of antibodies, which consist of single domain fragments. They have become of considerable interest as next-generation biotechnological tools for antigen recognition. They can be easily engineered due to their high stability and compact size. Nanobodies have three complementarity-determining regions, CDRs, which are enlarged to provide a similar binding surface to that of human immunoglobulins. Here, we propose a benchmark testing algorithm that uses 3D structures of already existing protein-nanobody complexes as initial structures followed by successive mutations on the CDR domains. The aim is to find optimum binding amino acids for hypervariable residues of CDRs. We use molecular dynamics simulations to compare the binding energies of the resulting complexes with that of the known complex and accept those that are improved by mutations. We use the MDM4-VH9 complex, (PDB id 2VYR), fructose-bisphosphate aldolase from Trypanosoma congolense (PDB id 5O0W) and human lysozyme (PDB id 4I0C) as benchmark complexes. By using this algorithm, better binding nanobodies can be generated in a short amount of time. We suggest that this method can complement existing immune and synthetic library-based methods, without a need for extensive experimentation or large libraries.
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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.