ArticlemAbs
CDR-H3 loop ensemble in solution - conformational selection upon antibody binding.
Article in mAbs. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 73 citations in OpenAlex.
- Antibody-drug conjugate engineering: from design to efficacy and safety.Signal transduction and targeted therapy · 2026Review
- Efficient generation of epitope-targeted antibodies with Germinal.Nature biotechnology · 2026Article
- A Risk-Tiered Validation Framework for Artificial Intelligence in Drug Discovery: From Reproducibility to Clinical Translation.International journal of molecular sciences · 2026Review
- Confidence scoring for deep learning-predicted antibody-antigen complexes: AntiConf as a precision-driven metric.Briefings in bioinformatics · 2026Article
- Phage Display Technology: Design, Library Construction, and Panning Strategies for Antibody Development.Biomolecules & therapeutics · 2026Review
- What does AlphaFold3 learn about antibody and nanobody docking, and what remains unsolved?mAbs · 2025Article
- Article
- Comparison of sequence- and structure-based antibody clustering approaches on simulated repertoire sequencing data.PLoS computational biology · 2025Article
- AI-augmented physics-based docking for antibody-antigen complex prediction.Bioinformatics (Oxford, England) · 2025Article
- RosettaHDX: Predicting antibody-antigen interaction from hydrogen-deuterium exchange mass spectrometry data.Journal of structural biology · 2025Article
- Predicting the conformational flexibility of antibody and T cell receptor complementarity-determining regions.Nature machine intelligence · 2025Article
- Applying computational protein design to therapeutic antibody discovery - current state and perspectives.Frontiers in immunology · 2025Review
- Extended Conformational Selection in the Antigen-Antibody Interaction of the PfAMA1 Protein.The journal of physical chemistry. B · 2024Article
- De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics.ACS chemical biology · 2024Article
- Crystal structure of the long Rib domain of the LPXTG-anchored surface protein from Limosilactobacillus reuteri.Acta crystallographica. Section F, Structural biology communications · 2024Article
- The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics.Journal of chemical theory and computation · 2024Article
- Leveraging Artificial Intelligence to Expedite Antibody Design and Enhance Antibody-Antigen Interactions.Bioengineering (Basel, Switzerland) · 2024Review
- Phage display assisted discovery of a pH-dependent anti-α-cobratoxin antibody from a natural variable domain library.Protein science : a publication of the Protein Society · 2023Article
- Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines.Antibodies (Basel, Switzerland) · 2023Review
- Enhanced antibody-antigen structure prediction from molecular docking using AlphaFold2.Scientific reports · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 3 countries.
Funding
Abstract
We analyzed pairs of protein-binding, peptide-binding and hapten-binding antibodies crystallized as complex and in the absence of the antigen with and without conformational differences upon binding in the complementarity-determining region (CDR)-H3 loop. Here, we introduce a molecular dynamics-based approach to capture a diverse conformational ensemble of the CDR-H3 loop in solution. The results clearly indicate that the inherently flexible CDR-H3 loop indeed needs to be characterized as a conformational ensemble. The conformational changes of the CDR-H3 loop in all antibodies investigated follow the paradigm of conformation selection, because we observe the experimentally determined binding competent conformation without the presence of the antigen within the ensemble of pre-existing conformational states in solution before binding. We also demonstrate for several examples that the conformation observed in the antibody crystal structure without antigen present is actually selected to bind the carboxyterminal tail region of the antigen-binding fragment (Fab). Thus, special care must be taken when characterizing antibody CDR-H3 loops by Fab X-ray structures, and the possibility that pre-existing conformations are present should always be considered.
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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.