ArticleScientific reports2015
DockTope: a Web-based tool for automated pMHC-I modelling.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources.Genomics, proteomics & bioinformatics · 2025Review
- The dawn of biophysical representations in computational immunology.QRB discovery · 2025Review
- RankMHC: Learning to Rank Class-I Peptide-MHC Structural Models.Journal of chemical information and modeling · 2024Article
- Unveiling cross-reactivity: implications for immune response modulation in cancer.Briefings in bioinformatics · 2024Article
- MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction.Biophysical journal · 2024Article
- APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries.Journal of chemical information and modeling · 2024Article
- Review
- MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction.bioRxiv : the preprint server for biology · 2023Article
- HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes.Nature communications · 2023Article
- PepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structure.Frontiers in immunology · 2023Article
- 3pHLA-score improves structure-based peptide-HLA binding affinity prediction.Scientific reports · 2022Article
- 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
- Viral immunogenic footprints conferring T cell cross-protection to SARS-CoV-2 and its variants.Frontiers in immunology · 2022Article
- MatchTope: A tool to predict the cross reactivity of peptides complexed with Major Histocompatibility Complex I.Frontiers in immunology · 2022Article
- Graph representation learning for structural proteomics.Emerging topics in life sciences · 2021Review
- Immunogenic T cell epitopes of SARS-CoV-2 are recognized by circulating memory and naïve CD8 T cells of unexposed individuals.EBioMedicine · 2021Article
- Can molecular mimicry explain the cytokine storm of SARS-CoV-2?: An in silico approach.Journal of medical virology · 2021Article
- Viral Molecular Mimicry Influences the Antitumor Immune Response in Murine and Human Melanoma.Cancer immunology research · 2021Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The immune system is constantly challenged, being required to protect the organism against a wide variety of infectious pathogens and, at the same time, to avoid autoimmune disorders. One of the most important molecules involved in these events is the Major Histocompatibility Complex class I (MHC-I), responsible for binding and presenting small peptides from the intracellular environment to CD8(+) T cells. The study of peptide:MHC-I (pMHC-I) molecules at a structural level is crucial to understand the molecular mechanisms underlying immunologic responses. Unfortunately, there are few pMHC-I structures in the Protein Data Bank (PDB) (especially considering the total number of complexes that could be formed combining different peptides), and pMHC-I modelling tools are scarce. Here, we present DockTope, a free and reliable web-based tool for pMHC-I modelling, based on crystal structures from the PDB. DockTope is fully automated and allows any researcher to construct a pMHC-I complex in an efficient way. We have reproduced a dataset of 135 non-redundant pMHC-I structures from the PDB (Cα RMSD below 1 Å). Modelling of pMHC-I complexes is remarkably important, contributing to the knowledge of important events such as cross-reactivity, autoimmunity, cancer therapy, transplantation and rational vaccine design.
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