ArticleBiotechnology and bioengineering2017
Computational de novo design of antibodies binding to a peptide with high affinity.
Article in Biotechnology and bioengineering, 2017. 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, 34 citations in OpenAlex.
- Antibody-drug conjugate engineering: from design to efficacy and safety.Signal transduction and targeted therapy · 2026Review
- A systematic evaluation framework for universal antibody-antigen binding affinity prediction and candidate recommendation.iScience · 2026Article
- Exploring Experimental and In Silico Approaches for Antibody-Drug Conjugates in Oncology Therapies.Pharmaceuticals (Basel, Switzerland) · 2025Review
- 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
- Revolutionizing Synthetic Antibody Design: Harnessing Artificial Intelligence and Deep Sequencing Big Data for Unprecedented Advances.Molecular biotechnology · 2025Review
- Applying computational protein design to therapeutic antibody discovery - current state and perspectives.Frontiers in immunology · 2025Review
- Targeting Ras-binding domain of ELMO1 by computational nanobody design.Communications biology · 2023Article
- Structural Classification of CDR-H3 in Single-Domain VMethods in molecular biology (Clifton, N.J.) · 2023Article
- Understanding and Modulating Antibody Fine Specificity: Lessons from Combinatorial Biology.Antibodies (Basel, Switzerland) · 2022Review
- Higher Affinity Antibodies Bind With Lower Hydration and Flexibility in Large Scale Simulations.Frontiers in immunology · 2022Article
- Redesigning an antibody H3 loop by virtual screening of a small library of human germline-derived sequences.Scientific reports · 2021Article
- IsAb: a computational protocol for antibody design.Briefings in bioinformatics · 2021Article
- Investigation of major amino acid residues of anti-norfloxacin monoclonal antibodies responsible for binding with fluoroquinolones.Scientific reports · 2021Article
- Concerns with computational protein engineering programmes IPRO and OptMAVEn and metabolic pathway engineering programme optStoic.Open biology · 2021Article
- Designing antibody against highly conserved region of dengue envelope protein by in silico screening of scFv mutant library.PloS one · 2019Article
- OptMAVEn-2.0: De novo Design of Variable Antibody Regions against Targeted Antigen Epitopes.Antibodies (Basel, Switzerland) · 2018Article
- RosettaAntibodyDesign (RAbD): A general framework for computational antibody design.PLoS computational biology · 2018Article
- De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide.Scientific reports · 2017Article
- Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
Antibody drugs play a critical role in infectious diseases, cancer, autoimmune diseases, and inflammation. However, experimental methods for the generation of therapeutic antibodies such as using immunized mice or directed evolution remain time consuming and cannot target a specific antigen epitope. Here, we describe the application of a computational framework called OptMAVEn combined with molecular dynamics to de novo design antibodies. Our reference system is antibody 2D10, a single-chain antibody (scFv) that recognizes the dodecapeptide DVFYPYPYASGS, a peptide mimic of mannose-containing carbohydrates. Five de novo designed scFvs sharing less than 75% sequence similarity to all existing natural antibody sequences were generated using OptMAVEn and their binding to the dodecapeptide was experimentally characterized by biolayer interferometry and isothermal titration calorimetry. Among them, three scFvs show binding affinity to the dodecapeptide at the nM level. Critically, these de novo designed scFvs exhibit considerably diverse modeled binding modes with the dodecapeptide. The results demonstrate the potential of OptMAVEn for the de novo design of thermally and conformationally stable antibodies with high binding affinity to antigens and encourage the targeting of other antigen targets in the future. Biotechnol. Bioeng. 2017;114: 1331-1342. © 2017 Wiley Periodicals, Inc.
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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.