ArticleStructure (London, England : 1993)2021
An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants.
Article in Structure (London, England : 1993), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 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
74 citing papers in PubMed.
- AlphaFold and Docking Approaches for Antibody-Antigen and Other Targets: Insights From CAPRI Rounds 47-55.Proteins · 2026Article
- Computational design and translational development of TCR-mimic scFv antibodies for peptide-HLA neoantigen targeting.npj drug discovery · 2026Review
- Phys-AbGAT: a physics-informed multi-task graph attention network for robust antibody-antigen binding affinity prediction.Bioinformatics (Oxford, England) · 2026Article
- A systematic evaluation framework for universal antibody-antigen binding affinity prediction and candidate recommendation.iScience · 2026Article
- Benchmarking AlphaFold and related deep learning approaches for modeling antibody and TCR antigen recognition.bioRxiv : the preprint server for biology · 2026Article
- BindPred: a framework for predicting protein-protein binding affinity from language model embeddings.Bioinformatics (Oxford, England) · 2026Article
- Improving protein and protein interactions using pseudo-dimers derived from monomeric proteins.Nature communications · 2026Article
- Biophysical trade-offs in antibody evolution are resolved by conformation-mediated epistasis.bioRxiv : the preprint server for biology · 2026Article
- Cell-Based Immunization Combined with Single-Round Cell Panning Enables Discovery of PSMA-Targeting Nanobodies from Phage Display Libraries.Biomolecules · 2026Article
- Ab-SELDON: Leveraging Diversity Data for an Efficient Automated Computational Pipeline for Antibody Design.Journal of chemical information and modeling · 2026Article
- Beyond contacts: The important role of the support region in protein complex assembly.Protein science : a publication of the Protein Society · 2026Article
- Article
- Computational models for the classification of antibody specificity using heavy chain features.PloS one · 2026Article
- CoV-UniBind: a unified antibody binding database for SARS-CoV-2.Bioinformatics advances · 2026Article
- Nanobodies in biomedicine: from molecular characteristics to fabrication and clinical translation.Military Medical Research · 2026Review
- Exploring antibody-antigen binding affinity using degree-based topological indices: a graph-theoretical approach.Frontiers in chemistry · 2026Article
- Modeling Protein-Protein Complexes by Combining pyDock and AlphaFold.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Can We Extract Physics-like Energies from Generative Protein Diffusion Models?bioRxiv : the preprint server for biology · 2025Article
- Review
- Structures of CRP antigen-antibody complexes provide insights into the mechanism of specific recognition.Communications biology · 2025Article
14 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Accurate predictive modeling of antibody-antigen complex structures and structure-based antibody design remain major challenges in computational biology, with implications for biotherapeutics, immunity, and vaccines. Through a systematic search for high-resolution structures of antibody-antigen complexes and unbound antibody and antigen structures, in conjunction with identification of experimentally determined binding affinities, we have assembled a non-redundant set of test cases for antibody-antigen docking and affinity prediction. This benchmark more than doubles the number of antibody-antigen complexes and corresponding affinities available in our previous benchmarks, providing an unprecedented view of the determinants of antibody recognition and insights into molecular flexibility. Initial assessments of docking and affinity prediction tools highlight the challenges posed by this diverse set of cases, which includes camelid nanobodies, therapeutic monoclonal antibodies, and broadly neutralizing antibodies targeting viral glycoproteins. This dataset will enable development of advanced predictive modeling and design methods for this therapeutically relevant class of protein-protein interactions.
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.