ArticleScientific reports2017
De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 37 citations in OpenAlex.
- Extracellular Peptide-Ligand Dimerization Actuator Receptor Design for Reversible and Spatially Dosed 3D Cell-Material Communication.ACS synthetic biology · 2025Article
- Using Short Molecular Dynamics Simulations to Determine the Important Features of Interactions in Antibody-Protein Complexes.Proteins · 2025Article
- Computational electrostatic engineering of nanobodies for enhanced SARS-CoV-2 receptor binding domain recognition.Frontiers in molecular biosciences · 2025Article
- A quantitative comparison of antibodies against epitope tags for immunofluorescence detection.FEBS open bio · 2023Article
- Structural Classification of CDR-H3 in Single-Domain VMethods in molecular biology (Clifton, N.J.) · 2023Article
- Fragment-based computational design of antibodies targeting structured epitopes.Science advances · 2022Article
- Understanding and Modulating Antibody Fine Specificity: Lessons from Combinatorial Biology.Antibodies (Basel, Switzerland) · 2022Review
- Redesigning an antibody H3 loop by virtual screening of a small library of human germline-derived sequences.Scientific reports · 2021Article
- Mass Spectrometry-BasedJournal of proteome research · 2021Article
- Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations.Journal of chemical theory and computation · 2019Article
- Designing antibody against highly conserved region of dengue envelope protein by in silico screening of scFv mutant library.PloS one · 2019Article
- Computational affinity maturation of camelid single-domain intrabodies against the nonamyloid component of alpha-synuclein.Scientific reports · 2018Article
- OptMAVEn-2.0: De novo Design of Variable Antibody Regions against Targeted Antigen Epitopes.Antibodies (Basel, Switzerland) · 2018Article
- Engineering therapeutic antibodies to combat infectious diseases.Current opinion in chemical engineering · 2018Article
- Article
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 1 country.
Funding
Abstract
Computational antibody engineering efforts to date have focused on improving binding affinities or biophysical characteristics. De novo design of antibodies binding specific epitopes could greatly accelerate discovery of therapeutics as compared to conventional immunization or synthetic library selection strategies. Here, we employed de novo complementarity determining region (CDR) design to engineer targeted antibody-antigen interactions using previously described in silico methods. CDRs predicted to bind the minimal FLAG peptide (Asp-Tyr-Lys-Asp) were grafted onto a single-chain variable fragment (scFv) acceptor framework. Fifty scFvs comprised of designed heavy and light or just heavy chain CDRs were synthesized and screened for peptide binding by phage ELISA. Roughly half of the designs resulted in detectable scFv expression. Four antibodies, designed entirely in silico, bound the minimal FLAG sequence with high specificity and sensitivity. When reformatted as soluble antigen-binding fragments (Fab), these clones expressed well, were predominantly monomeric and retained peptide specificity. In both formats, the antibodies bind the peptide only when present at the amino-terminus of a carrier protein and even conservative peptide amino acid substitutions resulted in a complete loss of binding. These results support in silico CDR design of antibody specificity as an emerging antibody engineering strategy.
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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.