ArticlemAbs
Hiding in plain sight: structure and sequence analysis reveals the importance of the antibody DE loop for antibody-antigen binding.
Article in mAbs. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed, 33 citations in OpenAlex.
- Tokenizing loops of antibodies.mAbs · 2026Article
- Adaptive Disorder as the Hallmark of Nanobodies Antigen-Binding Loops.Journal of chemical information and modeling · 2026Article
- ANARCII enables alignment-free antigen receptor numbering using a generalised language model.Communications biology · 2026Article
- Ab-SELDON: Leveraging Diversity Data for an Efficient Automated Computational Pipeline for Antibody Design.Journal of chemical information and modeling · 2026Article
- Paraplume: A fast and accurate antibody paratope prediction method provides insights into repertoire-scale binding dynamics.PLoS computational biology · 2026Article
- Strategies to Screen and Evaluate Brain Targeting Antibodies Using an iPSC-Derived Blood-Brain Barrier Model.Antibodies (Basel, Switzerland) · 2025Article
- A Sitewise Model of Natural Selection on Individual Antibodies via a Transformer-Encoder.Molecular biology and evolution · 2025Article
- Revolutionizing oncology: the role of Artificial Intelligence (AI) as an antibody design, and optimization tools.Biomarker research · 2025Review
- An explainable language model for antibody specificity prediction using curated influenza hemagglutinin antibodies.Immunity · 2024Article
- Epidemiological investigation and analysis of the infection of porcine circovirus in Xinjiang.Virology journal · 2024Article
- Unveiling the multifaceted landscape of N-glycosylation in antibody variable domains: Insights and implications.International journal of biological macromolecules · 2024Article
- Prospects for the computational humanization of antibodies and nanobodies.Frontiers in immunology · 2024Review
- HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes.Nature communications · 2023Article
- Arginine cluster introduction on framework region in anti-lysozyme antibody improved association rate constant by changing conformational diversity of CDR loops.Protein science : a publication of the Protein Society · 2023Article
- General Trends of theInternational journal of molecular sciences · 2023Article
- Structural Characterization of Nanobodies during Germline Maturation.Biomolecules · 2023Article
- Structural Classification of CDR-H3 in Single-Domain VMethods in molecular biology (Clifton, N.J.) · 2023Article
- A comparison of the binding sites of antibodies and single-domain antibodies.Frontiers in immunology · 2023Article
- Delineating the RAS Conformational Landscape.Cancer research · 2022Article
- Conformational Entropy as a Potential Liability of Computationally Designed Antibodies.Biomolecules · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
Abstract
Antibody variable domains contain "complementarity-determining regions" (CDRs), the loops that form the antigen binding site. CDRs1-3 are recognized as the canonical CDRs. However, a fourth loop sits adjacent to CDR1 and CDR2 and joins the D and E strands on the antibody v-type fold. This "DE loop" is usually treated as a framework region, even though mutations in the loop affect the conformation of the CDRs and residues in the DE loop occasionally contact antigen. We analyzed the length, structure, and sequence features of all DE loops in the Protein Data Bank (PDB), as well as millions of sequences from HIV-1 infected and naïve patients. We refer to the DE loop as H4 and L4 in the heavy and light chains, respectively. Clustering the backbone conformations of the most common length of L4 (6 residues) reveals four conformations: two κ-only clusters, one λ-only cluster, and one mixed κ/λ cluster. Most H4 loops are length-8 and exist primarily in one conformation; a secondary conformation represents a small fraction of H4-8 structures. H4 sequence variability exceeds that of the antibody framework in naïve human high-throughput sequences, and both L4 and H4 sequence variability from λ and heavy germline sequences exceed that of germline framework regions. Finally, we identified dozens of structures in the PDB with insertions in the DE loop, all related to broadly neutralizing HIV-1 antibodies (bNabs), as well as antibody sequences from high-throughput sequencing studies of HIV-infected individuals, illuminating a possible role in humoral immunity to HIV-1.
Indexed as
Identifiers
What OpenQuestion holds
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.