ArticleNature communications2023
HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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
23 citing papers in PubMed, 24 citations in OpenAlex.
- Cross-task interpretability through unified modeling reveals a universal shortcut bias in neoantigen prediction.Cell genomics · 2026Article
- A generalizable system for antigenic peptide targeting across HLA-I allotypes.bioRxiv : the preprint server for biology · 2026Article
- Dynamic Allostery in T Cell Receptor Specificity: A Role for Peptides and MHC Polymorphisms in Allosterically Tuning Immune Recognition.BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Comparative analysis of pan MHC‑I epitopes immunoreactivity on Hantaan virus nucleocapsid protein.International journal of molecular medicine · 2026Article
- Structural changes from wild-type define tumor-rejecting neoantigens.Journal for immunotherapy of cancer · 2025Article
- Targeting peptide antigens using a multiallelic MHC I-binding system.Nature biotechnology · 2025Article
- A structure-guided approach to predict MHC-I restriction of T cell receptors for public antigens.Structure (London, England : 1993) · 2025Article
- SimPep and OP-AND: A deep learning framework and curated database for predicting osteogenic peptides.PLoS computational biology · 2025Article
- Solution mapping of MHC-I:TCR interactions using a minimalistic protein system.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Identification and biophysical characterization of Plasmodium peptide binding by common African HLAs.Scientific reports · 2025Article
- Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity.Nature communications · 2025Article
- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
- RankMHC: Learning to Rank Class-I Peptide-MHC Structural Models.Journal of chemical information and modeling · 2024Article
- Strengths and limitations of web servers for the modeling of TCRpMHC complexes.Computational and structural biotechnology journal · 2024Article
- PepCARES: A Comprehensive Advanced Refinement and Evaluation System for Peptide Design and Affinity Screening.ACS omega · 2024Article
- TCR-T cell therapy: current development approaches, preclinical evaluation, and perspectives on regulatory challenges.Journal of translational medicine · 2024Review
- Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity.Research square · 2024Article
- Quantifying conformational changes in the TCR:pMHC-I binding interface.Frontiers in immunology · 2024Article
- Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Conformational plasticity of RAS Q61 family of neoepitopes results in distinct features for targeted recognition.Nature communications · 2023Article
Corrections and comments
- Update of
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
The class I proteins of the major histocompatibility complex (MHC-I) display epitopic peptides derived from endogenous proteins on the cell surface for immune surveillance. Accurate modeling of peptides bound to the human MHC, HLA, has been mired by conformational diversity of the central peptide residues, which are critical for recognition by T cell receptors. Here, analysis of X-ray crystal structures within our curated database (HLA3DB) shows that pHLA complexes encompassing multiple HLA allotypes present a discrete set of peptide backbone conformations. Leveraging these backbones, we employ a regression model trained on terms of a physically relevant energy function to develop a comparative modeling approach for nonamer pHLA structures named RepPred. Our method outperforms the top pHLA modeling approach by up to 19% in structural accuracy, and consistently predicts blind targets not included in our training set. Insights from our work may be applied towards predicting antigen immunogenicity, and receptor cross-reactivity.
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.