ArticleJCO clinical cancer informatics2020
HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy.
Article in JCO clinical cancer informatics, 2020. 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, 24 citations in OpenAlex.
- Computational prediction of TCR cross-reactivity: principles, challenges and translational opportunities.Journal of translational medicine · 2026Review
- Structural evolution of polymorphic class I HLA alleles, designating HLA-C with uncertain assemblies.Computational and structural biotechnology journal · 2026Article
- AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential.NPJ digital medicine · 2025Review
- Identification of immunogenic KIF5B-RET fusion neopeptides driving immune stimulation in tumor specific CD8+ T cells.Frontiers in immunology · 2025Article
- Article
- Mutations in glioblastoma proteins do not disrupt epitope presentation and recognition, maintaining a specific CD8 T cell immune response potential.Scientific reports · 2024Article
- Novel insights into TCR-T cell therapy in solid neoplasms: optimizing adoptive immunotherapy.Experimental hematology & oncology · 2024Review
- Article
- Computational Approaches Drive Developments in Immune-Oncology Therapies for PD-1/PD-L1 Immune Checkpoint Inhibitors.International journal of molecular sciences · 2023Review
- TCR-engineered T cell therapy in solid tumors: State of the art and perspectives.Science advances · 2023Review
- Physicochemical Heuristics for Identifying High Fidelity, Near-Native Structural Models of Peptide/MHC Complexes.Frontiers in immunology · 2022Article
- Structural Prediction of Peptide-MHC Binding Modes.Methods in molecular biology (Clifton, N.J.) · 2022Review
- PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes.Frontiers in immunology · 2022Article
- SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development.Frontiers in immunology · 2022Article
- DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins.Computers in biology and medicine · 2021Article
- Immunogenic T cell epitopes of SARS-CoV-2 are recognized by circulating memory and naïve CD8 T cells of unexposed individuals.EBioMedicine · 2021Article
- Large-Scale Structure-Based Screening of Potential T Cell Cross-Reactivities Involving Peptide-Targets From BCG Vaccine and SARS-CoV-2.Frontiers in immunology · 2021Article
- Markov state modeling reveals alternative unbinding pathways for peptide-MHC complexes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Informatics Tools for Cancer Research and Care: Bridging the Gap Between Innovation and Implementation.JCO clinical cancer informatics · 2020Article
- Structural Modeling and Molecular Dynamics of the Immune Checkpoint Molecule HLA-G.Frontiers in immunology · 2020Article
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
purposeHLA protein receptors play a key role in cellular immunity. They bind intracellular peptides and display them for recognition by T-cell lymphocytes. Because T-cell activation is partially driven by structural features of these peptide-HLA complexes, their structural modeling and analysis are becoming central components of cancer immunotherapy projects. Unfortunately, this kind of analysis is limited by the small number of experimentally determined structures of peptide-HLA complexes. Overcoming this limitation requires developing novel computational methods to model and analyze peptide-HLA structures.
methodsHere we describe a new platform for the structural modeling and analysis of peptide-HLA complexes, called HLA-Arena, which we have implemented using Jupyter Notebook and Docker. It is a customizable environment that facilitates the use of computational tools, such as APE-Gen and DINC, which we have previously applied to peptide-HLA complexes. By integrating other commonly used tools, such as MODELLER and MHCflurry, this environment includes support for diverse tasks in structural modeling, analysis, and visualization.
resultsTo illustrate the capabilities of HLA-Arena, we describe 3 example workflows applied to peptide-HLA complexes. Leveraging the strengths of our tools, DINC and APE-Gen, the first 2 workflows show how to perform geometry prediction for peptide-HLA complexes and structure-based binding prediction, respectively. The third workflow presents an example of large-scale virtual screening of peptides for multiple HLA alleles.
conclusionThese workflows illustrate the potential benefits of HLA-Arena for the structural modeling and analysis of peptide-HLA complexes. Because HLA-Arena can easily be integrated within larger computational pipelines, we expect its potential impact to vastly increase. For instance, it could be used to conduct structural analyses for personalized cancer immunotherapy, neoantigen discovery, or vaccine development.
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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.