ArticleScientific reports2016
Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Nanobody engineering: computational modelling and design for biomedical and therapeutic applications.FEBS open bio · 2025Review
- General Trends of theInternational journal of molecular sciences · 2023Article
- Protein purification strategies must consider downstream applications and individual biological characteristics.Microbial cell factories · 2022Review
- Computational Evolution Protocol for Peptide Design.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain VScientific reports · 2021Article
- Effect of Humanizing Mutations on the Stability of the Llama Single-Domain Variable Region.Biomolecules · 2021Article
- Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors.International journal of molecular sciences · 2021Article
- Recombinant expression of nanobodies and nanobody-derived immunoreagents.Protein expression and purification · 2020Review
- Homology Modeling-Based in Silico Affinity Maturation Improves the Affinity of a Nanobody.International journal of molecular sciences · 2019Article
- Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility.Nucleic acids research · 2019Article
- Novel Benzene-Based Carbamates for AChE/BChE Inhibition: Synthesis and Ligand/Structure-Oriented SAR Study.International journal of molecular sciences · 2019Article
- Enhanced Thermostability of Glucose Oxidase through Computer-Aided Molecular Design.International journal of molecular sciences · 2018Article
- Quantification of Circulating Cancer Biomarkers via Sensitive Topographic Measurements on Single Binder Nanoarrays.ACS omega · 2017Article
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3 authors.
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Abstract
Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular recognition. Their small size represents a precious advantage for rational mutagenesis based on modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate mutations by developing a simulation protocol based on all-atom molecular dynamics and whole-molecule docking. The method was tested on two sets of nanobodies characterized experimentally for their biophysical features. One set contained point mutations introduced to humanize a wild type sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae and human hallmarks. The method resulted in accurate scoring approaches to predict experimental yields and enabled to identify the structural modifications induced by mutations. This work is a promising tool for the in silico development of single-domain antibodies and opens the opportunity to customize single functional domains of larger macromolecules.
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