R3X217 last accessed: 2022-11-04

iedb-v2
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:38.998105

Other names: IEDB, Immune Epitope Database and Analysis Resource, iedb-v2

The IEDB provides the scientific community with a central repository of freely accessible epitope data and epitope prediction and analysis resources. The IEDB is a publicly accessible, comprehensive immune epitope database containing peptidic linear and conformational epitopes and non peptidic epitopes such as lipids, metals, drugs, carbohydrates, etc, with published or submitted antibody, T cell, MHC binding or MHC ligand elution experimental assays. Epitope data related to infectious diseases, allergy, autoimmunity and transplant tested in humans, non human primates, and any other species can be found in the IEDB.

Webpage:

http://www.iedb.org/

Licence:

Name: Public Domain
URL: https://www.iedb.org/terms_of_use_v3.php

Publications: (7)

Publications
More detailed information about this field from each metasource.

The immune epitope database (IEDB) 3.0
PMID: 25300482
metasource: Fairsharing.org
version: FAIRsharing.org: IEDB; Immune Epitope Database; DOI: https://doi.org/10.25504/FAIRsharing.c886cd; Last edited: April 14, 2020, 6 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

The immune epitope database 2.0
PMID: 19906713
metasource: Fairsharing.org
version: FAIRsharing.org: IEDB; Immune Epitope Database; DOI: https://doi.org/10.25504/FAIRsharing.c886cd; Last edited: April 14, 2020, 6 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

The immune epitope database and analysis resource: from vision to blueprint
PMID: 15760272
metasource: Fairsharing.org
version: FAIRsharing.org: IEDB; Immune Epitope Database; DOI: https://doi.org/10.25504/FAIRsharing.c886cd; Last edited: April 14, 2020, 6 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

The immune epitope database: a historical retrospective of the first decade
PMID: 22681406
metasource: Fairsharing.org
version: FAIRsharing.org: IEDB; Immune Epitope Database; DOI: https://doi.org/10.25504/FAIRsharing.c886cd; Last edited: April 14, 2020, 6 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

Conservation Analysis of B-Cell Allergen Epitopes to Predict Clinical Cross-Reactivity Between Shellfish and Inhalant Invertebrate Allergens
PMID: 31803189
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:38.998105

The immune epitope database and analysis resource: from vision to blueprint
PMID: 16312048
metasource: Fairsharing.org
version: FAIRsharing.org: IEDB; Immune Epitope Database; DOI: https://doi.org/10.25504/FAIRsharing.c886cd; Last edited: April 14, 2020, 6 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

http://dx.doi.org/10.1093/nar/gku938
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

The immune epitope database (IEDB) 3.0 PubMed citations: 443.

443 articles citing: The immune epitope database (IEDB) 3.0

Human Coronavirus Spike Protein Based Multi-Epitope Vaccine against COVID-19 and Potential Future Zoonotic Coronaviruses by Using Immunoinformatic Approaches. PMID:35891314
Reverse Vaccinology and Immunoinformatic Assisted Designing of a Multi-Epitopes Based Vaccine Against Nosocomial Burkholderia cepacia. PMID:35875518
In silico designing of a multi-epitope vaccine against Burkholderia pseudomallei: reverse vaccinology and immunoinformatics. PMID:35821357
Computer-Aided Multi-Epitope Vaccine Design against Enterobacter xiangfangensis. PMID:35805383
Development of Multi-epitope Based Subunit Vaccine Against Crimean-Congo Hemorrhagic Fever Virus Using Reverse Vaccinology Approach. PMID:35789799
Computational cancer neoantigen prediction: current status and recent advances. PMID:35755950
CAVES: A Novel Tool for Comparative Analysis of Variant Epitope Sequences. PMID:35746624
Immunoinformatic Design of a Multivalent Peptide Vaccine Against Mucormycosis: Targeting FTR1 Protein of Major Causative Fungi. PMID:35720422
A reverse vaccinology approach on transmembrane carbonic anhydrases from Plasmodium species as vaccine candidates for malaria prevention. PMID:35706028
HLA-B*57:01 Complexed to a CD8 T-Cell Epitope from the HSV-2 ICP22 Protein Binds NK and T Cells through KIR3DL1. PMID:35632760
Designing of a Novel Multi-Antigenic Epitope-Based Vaccine against E. hormaechei: An Intergraded Reverse Vaccinology and Immunoinformatics Approach. PMID:35632421
Development of Anticancer Peptides Using Artificial Intelligence and Combinational Therapy for Cancer Therapeutics. PMID:35631583
Resilience of Spike-Specific Immunity Induced by COVID-19 Vaccines against SARS-CoV-2 Variants. PMID:35625733
In silico design and analyses of a multi-epitope vaccine against Crimean-Congo hemorrhagic fever virus through reverse vaccinology and immunoinformatics approaches. PMID:35610299
Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol. PMID:35572587
Vaccinomics to Design a Multi-Epitopes Vaccine for Acinetobacter baumannii. PMID:35564967
dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR Recognition. PMID:35493528
Therapeutic Vaccines Targeting Neoantigens to Induce T-Cell Immunity against Cancers. PMID:35456701
HSV-2-Specific Human Female Reproductive Tract Tissue Resident Memory T Cells Recognize Diverse HSV Antigens. PMID:35432373
Adult Memory T Cell Responses to the Respiratory Syncytial Virus Fusion Protein During a Single RSV Season (2018-2019). PMID:35422803
Unsupervised Mining of HLA-I Peptidomes Reveals New Binding Motifs and Potential False Positives in the Community Database. PMID:35386688
Designing of a Recombinant Multi-Epitopes Based Vaccine against Enterococcus mundtii Using Bioinformatics and Immunoinformatics Approaches. PMID:35329417
NeoScore Integrates Characteristics of the Neoantigen:MHC Class I Interaction and Expression to Accurately Prioritize Immunogenic Neoantigens. PMID:35304420
Structural Prediction of Peptide-MHC Binding Modes. PMID:35298818
ImmuneData: an integrated data discovery system for immunology data repositories. PMID:35262674
Upstream open reading frames regulate translation of cancer-associated transcripts and encode HLA-presented immunogenic tumor antigens. PMID:35239002
Mutational signature profiling classifies subtypes of clinically different mismatch-repair-deficient tumours with a differential immunogenic response potential. PMID:35197584
T cell response to intact SARS-CoV-2 includes coronavirus cross-reactive and variant-specific components. PMID:35133988
The Perspective of DMPK on Recombinant Adeno-Associated Virus-Based Gene Therapy: Past Learning, Current Support, and Future Contribution. PMID:35102450
Positional SHAP (PoSHAP) for Interpretation of machine learning models trained from biological sequences. PMID:35089914
A Combinatorial in-silico, in-vitro and in-vivo Approach to Quantitatively Study Peptide Induced MHC Stability. PMID:35087915
Computational construction of a glycoprotein multi-epitope subunit vaccine candidate for old and new South-African SARS-CoV-2 virus strains. PMID:35071728
Multi-omic machine learning predictor of breast cancer therapy response. PMID:34875674
In Silico Model Estimates the Clinical Trial Outcome of Cancer Vaccines. PMID:34831269
Development of an in silico multi-epitope vaccine against SARS-COV-2 by précised immune-informatics approaches. PMID:34746365
BCEPS: A Web Server to Predict Linear B Cell Epitopes with Enhanced Immunogenicity and Cross-Reactivity. PMID:34685724
Towards A Novel Multi-Epitopes Chimeric Vaccine for Simulating Strong Immune Responses and Protection against Morganella morganii. PMID:34682706
Designing a Multi-Epitope Vaccine against Chlamydia trachomatis by Employing Integrated Core Proteomics, Immuno-Informatics and In Silico Approaches. PMID:34681096
Targeting public neoantigens for cancer immunotherapy. PMID:34676374
Epitope-specific anti-PrP antibody toxicity: a comparative in-silico study of human and mouse prion proteins. PMID:34632945
Natural and cryptic peptides dominate the immunopeptidome of atypical teratoid rhabdoid tumors. PMID:34599019
Circulation of three genotypes and identification of unique mutations in neutralizing epitopes of infectious bronchitis virus in chickens in Bangladesh. PMID:34480638
Personalized immunotherapy in cancer precision medicine. PMID:34369137
Immunopeptidomics-Guided Warehouse Design for Peptide-Based Immunotherapy in Chronic Lymphocytic Leukemia. PMID:34305947
Seq12, Seq12m, and Seq13m, peptide analogues of the spike glycoprotein shows antiviral properties against SARS-CoV-2: An in silico study through molecular docking, molecular dynamics simulation, and MM-PB/GBSA calculations. PMID:34305174
Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota. PMID:34282338
Altered Actinobacteria and Firmicutes Phylum Associated Epitopes in Patients With Parkinson's Disease. PMID:34276644
Predicting MHC-peptide binding affinity by differential boundary tree. PMID:34252932
Recent progress on MHC-I epitope prediction in tumor immunotherapy. PMID:34249407
Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches. PMID:34237135
Integrated Core Proteomics, Subtractive Proteomics, and Immunoinformatics Investigation to Unveil a Potential Multi-Epitope Vaccine against Schistosomiasis. PMID:34208663
Multi-Epitope Vaccine Design Using an Immunoinformatic Approach for SARS-CoV-2. PMID:34208061
NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II. PMID:34162981
Landscape and selection of vaccine epitopes in SARS-CoV-2. PMID:34127050
Deciphering Human Leukocyte Antigen Susceptibility Maps From Immunopeptidomics Characterization in Oncology and Infections. PMID:34123866
Conformational epitope matching and prediction based on protein surface spiral features. PMID:34058977
Combination of highly antigenic nucleoproteins to inaugurate a cross-reactive next generation vaccine candidate against Arenaviridae family. PMID:34041391
Epitope-Based Peptide Vaccine Design against Fructose Bisphosphate Aldolase of Candida glabrata: An Immunoinformatics Approach. PMID:34036109
In silico design and in vitro expression of novel multiepitope DNA constructs based on HIV-1 proteins and Hsp70 T-cell epitopes. PMID:33987776
Identification of linear epitopes on the flagellar proteins of Clostridioides difficile. PMID:33976336
HLA-A2.1-restricted ECM1-derived epitope LA through DC cross-activation priming CD8+ T and NK cells: a novel therapeutic tumour vaccine. PMID:33910591
A conserved region of Acinetobacter trimeric autotransporter adhesion, Ata, provokes suppression of Acinetobacter baumannii virulence. PMID:33907866
Web resources facilitate drug discovery in treatment of COVID-19. PMID:33892145
HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy. PMID:33858848
Linear B-Cell Epitope Prediction for In Silico Vaccine Design: A Performance Review of Methods Available via Command-Line Interface. PMID:33809918
Population-Predicted MHC Class II Epitope Presentation of SARS-CoV-2 Structural Proteins Correlates to the Case Fatality Rates of COVID-19 in Different Countries. PMID:33807854
Nano-Enabled COVID-19 Vaccines: Meeting the Challenges of Durable Antibody Plus Cellular Immunity and Immune Escape. PMID:33793189
Introduction of Non-natural Amino Acids Into T-Cell Epitopes to Mitigate Peptide-Specific T-Cell Responses. PMID:33777029
Peptide-based therapeutic cancer vaccine: Current trends in clinical application. PMID:33754407
T cell and antibody kinetics delineate SARS-CoV-2 peptides mediating long-term immune responses in COVID-19 convalescent individuals. PMID:33723016
A Multiepitope Peptide, rOmp22, Encapsulated in Chitosan-PLGA Nanoparticles as a Candidate Vaccine Against Acinetobacter baumannii Infection. PMID:33707942
Antigen-Specific Treatment Modalities in MS: The Past, the Present, and the Future. PMID:33679769
COVIEdb: A Database for Potential Immune Epitopes of Coronaviruses. PMID:33628169
The Peptide Vaccine of the Future. PMID:33583769
Immunoinformatics Approach for the Identification and Characterization of T Cell and B Cell Epitopes towards the Peptide-Based Vaccine against SARS-CoV-2. PMID:33546870
Comprehensive epitope mapping using polyclonally expanded human CD8 T cells and a two-step ELISpot assay for testing large peptide libraries. PMID:33529681
In-host population dynamics of Mycobacterium tuberculosis complex during active disease. PMID:33522489
In silico and in vitro Evaluation of Mimetic Peptides as Potential Antigen Candidates for Prophylaxis of Leishmaniosis. PMID:33520931
SARS-CoV-2 and other human coronaviruses: Mapping of protease recognition sites, antigenic variation of spike protein and their grouping through molecular phylogenetics. PMID:33497837
In Silico Identification of New Targets for Diagnosis, Vaccine, and Drug Candidates against Trypanosoma cruzi. PMID:33488847
Comparison of the SARS-CoV-2 (2019-nCoV) M protein with its counterparts of SARS-CoV and MERS-CoV species. PMID:33432259
Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics and in silico approaches. PMID:33351863
Rapid microsphere-assisted peptide screening (MAPS) of promiscuous MHCII-binding peptides in Zika virus envelope protein. PMID:33343002
Like Wings of a Bird: Functional Divergence and Complementarity between HLA-A and HLA-B Molecules. PMID:33320202
Protective multi-epitope candidate vaccine for urinary tract infection. PMID:33304840
An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-CoV-2. PMID:33299503
Cationic Polymers for the Delivery of the Ebola DNA Vaccine Encoding Artificial T-Cell Immunogen. PMID:33271964
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery. PMID:33268350
SARS-CoV-2 and Plasmodium falciparum common immunodominant regions may explain low COVID-19 incidence in the malaria-endemic belt. PMID:33230417
A multiple peptides vaccine against COVID-19 designed from the nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the immunoinformatics approach. PMID:33200089
iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features. PMID:33099033
Spike protein-based epitopes predicted against SARS-CoV-2 through literature mining. PMID:33052325
Exploration of surface glycoprotein to design multi-epitope vaccine for the prevention of Covid-19. PMID:33043110
Immunoinformatics approach to understand molecular interaction between multi-epitopic regions of SARS-CoV-2 spike-protein with TLR4/MD-2 complex. PMID:33039603
Main Strategies for the Identification of Neoantigens. PMID:33036391
Benchmarking evolutionary tinkering underlying human-viral molecular mimicry shows multiple host pulmonary-arterial peptides mimicked by SARS-CoV-2. PMID:33024578
SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition. PMID:32999467
High-resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display. PMID:32954318
Analysis of Putative Epitope Candidates of Mycobacterium tuberculosis Against Pakistani Human Leukocyte Antigen Background: An Immunoinformatic Study for the Development of Future Vaccine. PMID:32922244
Genome based evolutionary lineage of SARS-CoV-2 towards the development of novel chimeric vaccine. PMID:32882432
Combining Three-Dimensional Modeling with Artificial Intelligence to Increase Specificity and Precision in Peptide-MHC Binding Predictions. PMID:32878910
Vaccine design of coronavirus spike (S) glycoprotein in chicken: immunoinformatics and computational approaches. PMID:32869000
Antigen processing and presentation in cancer immunotherapy. PMID:32859742
Integrated genomic analysis reveals mutated ELF3 as a potential gallbladder cancer vaccine candidate. PMID:32839463
Identification B and T-Cell epitopes and functional exposed amino acids of S protein as a potential vaccine candidate against SARS-CoV-2/COVID-19. PMID:32835775
Comprehensive genome based analysis of Vibrio parahaemolyticus for identifying novel drug and vaccine molecules: Subtractive proteomics and vaccinomics approach. PMID:32813697
Specificity of the T Cell Response to Protein Biopharmaceuticals. PMID:32793213
Designing Multi-Epitope Vaccines to Combat Emerging Coronavirus Disease 2019 (COVID-19) by Employing Immuno-Informatics Approach. PMID:32754160
Proteome-Wide Zika Virus CD4 T Cell Epitope and HLA Restriction Determination. PMID:32753403
A Pan-Specific GRU-Based Recurrent Neural Network for Predicting HLA-I-Binding Peptides. PMID:32743207
SARS-CoV-2 and Guillain-Barré syndrome: molecular mimicry with human heat shock proteins as potential pathogenic mechanism. PMID:32729001
Advances in Fungal Peptide Vaccines. PMID:32722452
Deep learning methods improve linear B-cell epitope prediction. PMID:32699555
T-Cell Dependent Immunogenicity of Protein Therapeutics Pre-clinical Assessment and Mitigation-Updated Consensus and Review 2020. PMID:32695107
Structure-based drug designing and immunoinformatics approach for SARS-CoV-2. PMID:32691011
HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy. PMID:32667823
MHCAttnNet: predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model. PMID:32657386
Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective. PMID:32622082
Nanomedicine and Onco-Immunotherapy: From the Bench to Bedside to Biomarkers. PMID:32610601
Landscape and Selection of Vaccine Epitopes in SARS-CoV-2. PMID:32577654
Impact of Cysteine Residues on MHC Binding Predictions and Recognition by Tumor-Reactive T Cells. PMID:32571843
Cancer Moonshot Immuno-Oncology Translational Network (IOTN): accelerating the clinical translation of basic discoveries for improving immunotherapy and immunoprevention of cancer. PMID:32554617
Dendritic Cell-Based Therapy Using LY6E Peptide with a Putative Role Against Colorectal Cancer. PMID:32548075
Personalized neoantigen vaccination with synthetic long peptides: recent advances and future perspectives. PMID:32483434
Is molecular mimicry the culprit in the autoimmune haemolytic anaemia affecting patients with COVID-19? PMID:32453861
Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system. PMID:32453790
Sequence-structure-function relationships in class I MHC: A local frustration perspective. PMID:32421728
Study of the Binding Pattern of HLA Class I Alleles of Indian Frequency and cTAP Binding Peptide for Chikungunya Vaccine Development. PMID:32421074
Heterogeneity of neoantigen landscape between primary lesions and their matched metastases in lung cancer. PMID:32420064
High throughput and comprehensive approach to develop multiepitope vaccine against minacious COVID-19. PMID:32417398
Preclinical Studies of the Off-Target Reactivity of AFP158-Specific TCR Engineered T Cells. PMID:32395117
The Bioinformatic and In Vitro Studies of Clostridioides Difficile Aminopeptidase M24 Revealed the Immunoreactive KKGIK Peptide. PMID:32392707
Epitope-Based Peptide Vaccine against Glycoprotein G of Nipah Henipavirus Using Immunoinformatics Approaches. PMID:32377531
In-silico identification of the vaccine candidate epitopes against the Lassa virus hemorrhagic fever. PMID:32376973
Molecular mimicry between SARS-CoV-2 and respiratory pacemaker neurons. PMID:32361194
A Review of Deep Learning Methods for Antibodies. PMID:32354020
Disordered epitopes as peptide vaccines. PMID:32328540
Computational Modeling and Analysis to Predict Intracellular Parasite Epitope Characteristics Using Random Forest Technique. PMID:32309231
Radiation-induced small extracellular vesicles as "carriages" promote tumor antigen release and trigger antitumor immunity. PMID:32308755
ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection. PMID:32241270
Prevalent and Diverse Intratumoral Oncoprotein-Specific CD8+ T Cells within Polyomavirus-Driven Merkel Cell Carcinomas. PMID:32179557
Harnessing neoantigen specific CD4 T cells for cancer immunotherapy. PMID:32170883
Hybrid Antigens Expressing Surface Loops of ZnuD From Acinetobacter baumannii Is Capable of Inducing Protection Against Infection. PMID:32117294
dbPepNeo: a manually curated database for human tumor neoantigen peptides. PMID:32090262
Predicting clinical benefit of immunotherapy by antigenic or functional mutations affecting tumour immunogenicity. PMID:32075964
A possible role for autoimmunity through molecular mimicry in alphavirus mediated arthritis. PMID:31969581
BioDADPep: A Bioinformatics database for anti diabetic peptides. PMID:31902976
Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design. PMID:31874646
High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets. PMID:31871119
Neoantigen Fitness Model Predicts Lower Immune Recognition of Cutaneous Squamous Cell Carcinomas Than Actinic Keratoses. PMID:31849976
Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands. PMID:31848261
A large peptidome dataset improves HLA class I epitope prediction across most of the human population. PMID:31844290
Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands. PMID:31824508
Computational assembly of a human Cytomegalovirus vaccine upon experimental epitope legacy. PMID:31823715
Constrained De Novo Sequencing of neo-Epitope Peptides using Tandem Mass Spectrometry. PMID:31819927
Considering Genomic and Immunological Correlates of Protection for a Dengue Intervention. PMID:31816907
Immunoinformatics Approach for Multiepitope Vaccine Prediction from H, M, F, and N Proteins of Peste des Petits Ruminants Virus. PMID:31781679
Identification and ranking of recurrent neo-epitopes in cancer. PMID:31775766
pMHC Structural Comparisons as a Pivotal Element to Detect and Validate T-Cell Targets for Vaccine Development and Immunotherapy-A New Methodological Proposal. PMID:31766602
The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook. PMID:31761977
An overview of immunoinformatics approaches and databases linking T cell receptor repertoires to their antigen specificity. PMID:31741011
Mapping Epitopes of a Novel Peptidoglycan Cross-Linking Enzyme Cwp22 Recognized by Human Sera Obtained from Patients with Clostridioides difficile Infection and Cord Blood. PMID:31739602
DeepHLApan: A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity. PMID:31736974
A comprehensive analysis of amino-peptidase N1 protein (APN) from Anopheles culicifacies for epitope design using Immuno-informatics models. PMID:31719771
TCR Fingerprinting and Off-Target Peptide Identification. PMID:31695703
Predicting HLA class II antigen presentation through integrated deep learning. PMID:31611695
Neoantigen Dissimilarity to the Self-Proteome Predicts Immunogenicity and Response to Immune Checkpoint Blockade. PMID:31606370
TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes. PMID:31601838
Rapid selection and identification of functional CD8+ T cell epitopes from large peptide-coding libraries. PMID:31591401
Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework. PMID:31591261
Next-generation computational tools for interrogating cancer immunity. PMID:31515541
Tumor neoantigens: from basic research to clinical applications. PMID:31492199
Improvement of Epitope Prediction Using Peptide Sequence Descriptors and Machine Learning. PMID:31491969
A general approach for predicting protein epitopes targeted by antibody repertoires using whole proteomes. PMID:31490930
The new identified biomarkers determine sensitivity to immune check-point blockade therapies in melanoma. PMID:31413919
Preliminary studies on development of a novel subunit vaccine targeting Clostridium perfringens mucolytic enzymes for the control of necrotic enteritis in broilers. PMID:31392320
Computational Analysis of HLA-presentation of Non-synonymous Recipient Mismatches Indicates Effect on the Risk of Chronic Graft-vs.-Host Disease After Allogeneic HSCT. PMID:31379830
Optimization of a nicotine degrading enzyme for potential use in treatment of nicotine addiction. PMID:31375100
Peptide-Based Subunit Vaccine Design of T- and B-Cells Multi-Epitopes against Zika Virus Using Immunoinformatics Approaches. PMID:31370224
Identification of Novel Respiratory Syncytial Virus CD4+ and CD8+ T Cell Epitopes in C57BL/6 Mice. PMID:31356172
Evaluating a Multiscale Mechanistic Model of the Immune System to Predict Human Immunogenicity for a Biotherapeutic in Phase 1. PMID:31342199
Immune-orthogonal orthologues of AAV capsids and of Cas9 circumvent the immune response to the administration of gene therapy. PMID:31332341
Delineating the Plausible Molecular Vaccine Candidates and Drug Targets of Multidrug-Resistant Acinetobacter baumannii. PMID:31281799
A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction. PMID:31204427
Cross-Reactivity as a Mechanism Linking Infections to Stroke. PMID:31156531
The Immune Contexture Associates with the Genomic Landscape in Lung Adenomatous Premalignancy. PMID:31142513
MHCSeqNet: a deep neural network model for universal MHC binding prediction. PMID:31138107
The expanding role of systems immunology in decoding the T cell receptor repertoire. PMID:31106281
HLA associations in inflammatory arthritis: emerging mechanisms and clinical implications. PMID:31092910
Delineating Surface Epitopes of Lyme Disease Pathogen Targeted by Highly Protective Antibodies of New Zealand White Rabbits. PMID:31085705
The combination of neoantigen quality and T lymphocyte infiltrates identifies glioblastomas with the longest survival. PMID:31044160
Genome-Wide Approach to the CD4 T-Cell Response to Human Herpesvirus 6B. PMID:31043533
Multifunctional CRISPR-Cas9 with engineered immunosilenced human T cell epitopes. PMID:31015529
Immunoinformatics Approach for Multiepitopes Vaccine Prediction against Glycoprotein B of Avian Infectious Laryngotracheitis Virus. PMID:31011331
First Evidence of Antibodies Against Lloviu Virus in Schreiber's Bent-Winged Insectivorous Bats Demonstrate a Wide Circulation of the Virus in Spain. PMID:31010201
Vive la difference! Self/non-self recognition and the evolution of signatures of identity in arms races with parasites. PMID:30967089
Comprehensive Review of Human Plasmodium falciparum-Specific CD8+ T Cell Epitopes. PMID:30949162
Design and molecular dynamic simulation of a new double-epitope tolerogenic protein as a potential vaccine for multiple sclerosis disease. PMID:30936929
In silico Designed Ebola Virus T-Cell Multi-Epitope DNA Vaccine Constructions Are Immunogenic in Mice. PMID:30934980
Genomic epidemiology of erythromycin-resistant Bordetella pertussis in China. PMID:30898080
Antibody Specific B-Cell Epitope Predictions: Leveraging Information From Antibody-Antigen Protein Complexes. PMID:30863406
Protein-Catalyzed Capture Agents. PMID:30838853
Pro-inflammatory Cytokines Alter the Immunopeptidome Landscape by Modulation of HLA-B Expression. PMID:30833945
Evidence for Highly Variable, Region-Specific Patterns of T-Cell Epitope Mutations Accumulating in Mycobacterium tuberculosis Strains. PMID:30814998
Successive crystal structure snapshots suggest the basis for MHC class I peptide loading and editing by tapasin. PMID:30808808
Most viral peptides displayed by class I MHC on infected cells are immunogenic. PMID:30718433
Pathogen diversity drives the evolution of generalist MHC-II alleles in human populations. PMID:30703088
T cell antigen discovery via signaling and antigen-presenting bifunctional receptors. PMID:30700902
DeepSeqPan, a novel deep convolutional neural network model for pan-specific class I HLA-peptide binding affinity prediction. PMID:30692623
Deimmunizing substitutions in Pseudomonas exotoxin domain III perturb antigen processing without eliminating T-cell epitopes. PMID:30683694
Perspective: The promises of a holistic view of proteins-impact on antibody engineering and drug discovery. PMID:30630879
Reduced bonobo MHC class I diversity predicts a reduced viral peptide binding ability compared to chimpanzees. PMID:30630404
Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome. PMID:30611210
Synthetic biology for bioengineering virus-like particle vaccines. PMID:30597533
GLUE: a flexible software system for virus sequence data. PMID:30563445
Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification. PMID:30556813
Epitope-Based Peptide Vaccine Against Fructose-Bisphosphate Aldolase of Madurella mycetomatis Using Immunoinformatics Approaches. PMID:30542244
Specific MHC-I Peptides Are Induced Using PROTACs. PMID:30524438
Epitope Specific Antibodies and T Cell Receptors in the Immune Epitope Database. PMID:30515166
Accounting for proximal variants improves neoantigen prediction. PMID:30510237
Footprints of antigen processing boost MHC class II natural ligand predictions. PMID:30446001
PRBAM: a new tool to analyze the MHC class I and HLA-DR anchor motifs. PMID:30408168
Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes. PMID:30408041
Human Disease Ontology 2018 update: classification, content and workflow expansion. PMID:30407550
The nature of the human T cell response to the cancer antigen 5T4 is determined by the balance of regulatory and inflammatory T cells of the same antigen-specificity: implications for vaccine design. PMID:30406375
Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition. PMID:30399156
Exploring NS3/4A, NS5A and NS5B proteins to design conserved subunit multi-epitope vaccine against HCV utilizing immunoinformatics approaches. PMID:30382118
Predicting T cell recognition of MHC class I restricted neoepitopes. PMID:30377561
The Immune Epitope Database (IEDB): 2018 update. PMID:30357391
A comprehensive in silico analysis for identification of therapeutic epitopes in HPV16, 18, 31 and 45 oncoproteins. PMID:30356257
Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes. PMID:30349087
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Genomic coordinates and continental distribution of 120 blood group variants reported by the 1000 Genomes Project. PMID:30312480
Peanut-specific T cell responses in patients with different clinical reactivity. PMID:30304054
Systematic identification of cancer-specific MHC-binding peptides with RAVEN. PMID:30228952
Epitopes identified in GAPDH from Clostridium difficile recognized as common antigens with potential autoimmunizing properties. PMID:30224677
TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis. PMID:30223042
When designing vaccines, consider the starting material: the human B cell repertoire. PMID:30190230
Linear epitopes in Onchocerca volvulus vaccine candidate proteins and excretory-secretory proteins. PMID:30188578
Pan-Genomic Study of Mycobacterium tuberculosis Reflecting the Primary/Secondary Genes, Generality/Individuality, and the Interconversion Through Copy Number Variations. PMID:30177918
Development and characterization of a novel monoclonal antibody that recognizes an epitope in the central protein interaction domain of RapGEF1 (C3G). PMID:30143974
Determination of a Predictive Cleavage Motif for Eluted Major Histocompatibility Complex Class II Ligands. PMID:30127785
PIP-EL: A New Ensemble Learning Method for Improved Proinflammatory Peptide Predictions. PMID:30108593
A Role for Epitope Networking in Immunomodulation by Helminths. PMID:30108588
Schistosoma mansoni SmKI-1 or Its C-Terminal Fragment Induces Partial Protection Against S. mansoni Infection in Mice. PMID:30105029
iBCE-EL: A New Ensemble Learning Framework for Improved Linear B-Cell Epitope Prediction. PMID:30100904
Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures. PMID:30100185
Predicting Antigen Presentation-What Could We Learn From a Million Peptides? PMID:30090105
Differing epidemiological dynamics of Chikungunya virus in the Americas during the 2014-2015 epidemic. PMID:30059496
Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches. PMID:30050166
The role of proteomics in the age of immunotherapies. PMID:30046851
Analysis of CD8+ T cell response during the 2013-2016 Ebola epidemic in West Africa. PMID:30038008
Novel frontiers in detecting cancer metastasis. PMID:30022365
Development of a novel clustering tool for linear peptide sequences. PMID:30014462
Genome-wide association and HLA fine-mapping studies identify risk loci and genetic pathways underlying allergic rhinitis. PMID:30013184
Peptide presentation by HLA-DQ molecules is associated with the development of immune tolerance. PMID:30002966
Trans-Allelic Model for Prediction of Peptide:MHC-II Interactions. PMID:29988560
Predicting HLA CD4 Immunogenicity in Human Populations. PMID:29963059
A clinically applicable adjuvant for an atherosclerosis vaccine in mice. PMID:29932463
Prediction of T-cell epitopes for designing a reverse vaccine against streptococcal bacteria. PMID:29911121
LeptoDB: an integrated database of genomics and proteomics resource of Leptospira. PMID:29905762
Divergent Allele Advantage at Human MHC Genes: Signatures of Past and Ongoing Selection. PMID:29893875
Postgenomic Approaches and Bioinformatics Tools to Advance the Development of Vaccines against Bacteria of the Burkholderia cepacia Complex. PMID:29890657
ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins. PMID:29878047
Identification of Surface Epitopes Associated with Protection against Highly Immune-Evasive VlsE-Expressing Lyme Disease Spirochetes. PMID:29866906
DNA immunization site determines the level of gene expression and the magnitude, but not the type of the induced immune response. PMID:29864114
Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. PMID:29855388
Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins. PMID:29782520
Nature of tumour rejection antigens in ovarian cancer. PMID:29772069
Higher baseline viral diversity correlates with lower HBsAg decline following PEGylated interferon-alpha therapy in patients with HBeAg-positive chronic hepatitis B. PMID:29765238
Update on Tumor Neoantigens and Their Utility: Why It Is Good to Be Different. PMID:29751996
Microbiota epitope similarity either dampens or enhances the immunogenicity of disease-associated antigenic epitopes. PMID:29734356
The C-terminal extension landscape of naturally presented HLA-I ligands. PMID:29712860
Cross-sectional analysis of CD8 T cell immunity to human herpesvirus 6B. PMID:29698478
Complexity of type-specific 56 kDa antigen CD4 T-cell epitopes of Orientia tsutsugamushi strains causing scrub typhus in India. PMID:29698425
AntiTbPdb: a knowledgebase of anti-tubercular peptides. PMID:29688365
Identification of errors in the IEDB using ontologies. PMID:29688357
FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. PMID:29688354
Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry. PMID:29658117
Peptide Sharing Between Viruses and DLX Proteins: A Potential Cross-Reactivity Pathway to Neuropsychiatric Disorders. PMID:29618965
NetH2pan: A Computational Tool to Guide MHC Peptide Prediction on Murine Tumors. PMID:29615400
Trypanosoma cruzi 80 kDa prolyl oligopeptidase (Tc80) as a novel immunogen for Chagas disease vaccine. PMID:29601585
Frequency of Interferon-Resistance Conferring Substitutions in Amino Acid Positions 70 and 91 of Core Protein of the Russian HCV 1b Isolates Analyzed in the T-Cell Epitopic Context. PMID:29577052
Immunomolecular Characterization of MIC-1, a Novel Antigen in Babesia bigemina, Which Contains Conserved and Immunodominant B-Cell Epitopes that Induce Neutralizing Antibodies. PMID:29570654
Low HLA binding of diabetes-associated CD8+ T-cell epitopes is increased by post translational modifications. PMID:29562882
Role of genetic heterogeneity in determining the epidemiological severity of H1N1 influenza. PMID:29561846
In silico prediction of cancer immunogens: current state of the art. PMID:29544447
General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept. PMID:29531253
Current progress of immunoinformatics approach harnessed for cellular- and antibody-dependent vaccine design. PMID:29528265
Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires. PMID:29515569
Cross-modality deep learning-based prediction of TAP binding and naturally processed peptide. PMID:29492592
Allergen and Epitope Targets of Mouse-Specific T Cell Responses in Allergy and Asthma. PMID:29487600
Protective Effect of Human Leukocyte Antigen (HLA) Allele DRB1*13:02 on Age-Related Brain Gray Matter Volume Reduction in Healthy Women. PMID:29452862
Prostaglandin D2 Receptor DP1 Antibodies Predict Vaccine-induced and Spontaneous Narcolepsy Type 1: Large-scale Study of Antibody Profiling. PMID:29449194
Fundamentals and Methods for T- and B-Cell Epitope Prediction. PMID:29445754
A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations. PMID:29441070
Identification of a Novel CD8 T Cell Epitope Derived from Plasmodium berghei Protective Liver-Stage Antigen. PMID:29434602
Mapping HLA-A2, -A3 and -B7 supertype-restricted T-cell epitopes in the ebolavirus proteome. PMID:29363421
Computational Tools for the Identification and Interpretation of Sequence Motifs in Immunopeptidomes. PMID:29327813
In silico epitope mapping and experimental evaluation of the Merozoite Adhesive Erythrocytic Binding Protein (MAEBL) as a malaria vaccine candidate. PMID:29316918
Improved methods for predicting peptide binding affinity to MHC class II molecules. PMID:29315598
The Role of Mass Spectrometry and Proteogenomics in the Advancement of HLA Epitope Prediction. PMID:29314742
Immunopharmacogenomics towards personalized cancer immunotherapy targeting neoantigens. PMID:29288513
Expitope 2.0: a tool to assess immunotherapeutic antigens for their potential cross-reactivity against naturally expressed proteins in human tissues. PMID:29282079
Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction. PMID:29281985
An automated benchmarking platform for MHC class II binding prediction methods. PMID:29281002
Informatics for cancer immunotherapy. PMID:29253114
Preclinical and clinical development of neoantigen vaccines. PMID:29253113
Live Attenuated Influenza Vaccines engineered to express the nucleoprotein of a recent isolate stimulate human influenza CD8+ T cells more relevant to current infections. PMID:29252117
High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome. PMID:29242379
Cloning, expression and purification of a polytopic antigen comprising of surface antigens of Toxoplasma gondii. PMID:29238461
AllerBase: a comprehensive allergen knowledgebase. PMID:29220458
Computationally-driven identification of antibody epitopes. PMID:29199956
IL17eScan: A Tool for the Identification of Peptides Inducing IL-17 Response. PMID:29163505
A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy. PMID:29132144
MHC-I Genotype Restricts the Oncogenic Mutational Landscape. PMID:29107334
Discovery of T-cell Driven Subunit Vaccines from Zika Virus Genome: An Immunoinformatics Approach. PMID:29094318
Analysis of predicted B and T-cell epitopes in Der p 23, allergen from Dermatophagoides pteronyssinus. PMID:29081610
Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy. PMID:29046675
The SysteMHC Atlas project. PMID:28985418
DRREP: deep ridge regressed epitope predictor. PMID:28984193
NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data. PMID:28978689
VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. PMID:28977646
Mutational Analysis of Gene Fusions Predicts Novel MHC Class I-Restricted T-Cell Epitopes and Immune Signatures in a Subset of Prostate Cancer. PMID:28954787
High somatic mutation and neoantigen burden are correlated with decreased progression-free survival in multiple myeloma. PMID:28937974
Viral based vaccine TG4010 induces broadening of specific immune response and improves outcome in advanced NSCLC. PMID:28923084
Induction of Paralysis and Visual System Injury in Mice by T Cells Specific for Neuromyelitis Optica Autoantigen Aquaporin-4. PMID:28872108
The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule. PMID:28855257
Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient. PMID:28841418
Development of a strategy and computational application to select candidate protein analogues with reduced HLA binding and immunogenicity. PMID:28833085
Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity. PMID:28832583
On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition. PMID:28779185
Tools to define the melanoma-associated immunopeptidome. PMID:28755382
Sharpening the Edge for Precision Cancer Immunotherapy: Targeting Tumor Antigens through Oncolytic Vaccines. PMID:28751892
The ADAMTS131239-1253 peptide is a dominant HLA-DR1-restricted CD4+ T-cell epitope. PMID:28751567
Discovery of a microbial transglutaminase enabling highly site-specific labeling of proteins. PMID:28751378
Detection of brain-directed autoantibodies in the serum of non-small cell lung cancer patients. PMID:28746384
Identification of putative unique immunogenic ZIKV and DENV1-4 peptides for diagnostic cellular based tests. PMID:28740150
Genotype-specific acquisition, evolution and adaptation of characteristic mutations in hepatitis E virus. PMID:28727933
Epitope determination of immunogenic proteins of Neisseria gonorrhoeae. PMID:28723967
Identification of Natural Regulatory T Cell Epitopes Reveals Convergence on a Dominant Autoantigen. PMID:28709804
Dual non-contiguous peptide occupancy of HLA class I evoke antiviral human CD8 T cell response and form neo-epitopes with self-antigens. PMID:28698575
A Fast and Inexpensive Protocol for Empirical Verification of Neutralizing Epitopes in Microbial Toxins and Enzymes. PMID:28660200
MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory. PMID:28650961
T cells from patients with Parkinson's disease recognize α-synuclein peptides. PMID:28636593
The Immune Epitope Database: How Data Are Entered and Retrieved. PMID:28634590
NOG-hIL-4-Tg, a new humanized mouse model for producing tumor antigen-specific IgG antibody by peptide vaccination. PMID:28617827
Identification of diagnostic peptide regions that distinguish Zika virus from related mosquito-borne Flaviviruses. PMID:28562637
Machine learning reveals a non-canonical mode of peptide binding to MHC class II molecules. PMID:28542831
Structural Definition of Duck Major Histocompatibility Complex Class I Molecules That Might Explain Efficient Cytotoxic T Lymphocyte Immunity to Influenza A Virus. PMID:28490583
ImmunoNodes - graphical development of complex immunoinformatics workflows. PMID:28482806
CancerPDF: A repository of cancer-associated peptidome found in human biofluids. PMID:28473704
BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. PMID:28472356
Pathogenic CD4+ T cells in patients with asthma. PMID:28442213
NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions. PMID:28407117
Computational Identification and Characterization of a Promiscuous T-Cell Epitope on the Extracellular Protein 85B of Mycobacterium spp. for Peptide-Based Subunit Vaccine Design. PMID:28401156
The Bioinformatics Analysis of Comparative Genomics of Mycobacterium tuberculosis Complex (MTBC) Provides Insight into Dissimilarities between Intraspecific Groups Differing in Host Association, Virulence, and Epitope Diversity. PMID:28377903
Proteomic analysis of protein purified derivative of Mycobacterium bovis. PMID:28372590
The Influence of HIV on the Evolution of Mycobacterium tuberculosis. PMID:28369607
Better living through ontologies at the Immune Epitope Database. PMID:28365732
The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design. PMID:28352270
Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens. PMID:28329770
PSSMHCpan: a novel PSSM-based software for predicting class I peptide-HLA binding affinity. PMID:28327987
Recent advances in Major Histocompatibility Complex (MHC) class I antigen presentation: Plastic MHC molecules and TAPBPR-mediated quality control. PMID:28299193
Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates. PMID:28248221
Immunogenicity of a Multi-Epitope DNA Vaccine Encoding Epitopes from Cu-Zn Superoxide Dismutase and Open Reading Frames of Brucella abortus in Mice. PMID:28232837
Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction. PMID:28228285
Identification of the core regulators of the HLA I-peptide binding process. PMID:28211542
Computer-aided designing of immunosuppressive peptides based on IL-10 inducing potential. PMID:28211521
Unconventional Peptide Presentation by Major Histocompatibility Complex (MHC) Class I Allele HLA-A*02:01: BREAKING CONFINEMENT. PMID:28179428
ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes. PMID:28160322
Patterns of Cellular Immunity Associated with Experimental Infection with rDEN2Δ30 (Tonga/74) Support Its Suitability as a Human Dengue Virus Challenge Strain. PMID:28148797
Evidence of an Antimicrobial Peptide Signature Encrypted in HECT E3 Ubiquitin Ligases. PMID:28119686
ArrayPitope: Automated Analysis of Amino Acid Substitutions for Peptide Microarray-Based Antibody Epitope Mapping. PMID:28095436
A Bioinformatics Practicum to Develop Student Understanding of Immunological Rejection of Protein Drugs. PMID:28090096
Definition of Human Epitopes Recognized in Tetanus Toxoid and Development of an Assay Strategy to Detect Ex Vivo Tetanus CD4+ T Cell Responses. PMID:28081174
Mycobacterium tuberculosis Complex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition. PMID:28062754
Transcriptomic analysis of human norovirus NS1-2 protein highlights a multifunctional role in murine monocytes. PMID:28056773
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Identifying Candidate Targets of Immune Responses in Zika Virus Based on Homology to Epitopes in Other Flavivirus Species. PMID:28018746
Immunodominance in allergic T-cell reactivity to Japanese cedar in different geographic cohorts. PMID:27979027
Tolerance checkpoint bypass permits emergence of pathogenic T cells to neuromyelitis optica autoantigen aquaporin-4. PMID:27940915
Screening and Identification of an H-2Kb-Restricted CTL Epitope within the Glycoprotein of Hantaan Virus. PMID:27933274
In silico Identification of Potential Peptides or Allergen Shot Candidates Against Aspergillus fumigatus. PMID:27872794
Immunoinformatics Approach in Designing Epitope-based Vaccine Against Meningitis-inducing Bacteria (Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae Type b). PMID:27812281
Role of HLA-DP in the Presentation of Epitopes from the Truncated Bacterial PE38 Immunotoxin. PMID:27796910
Immunoproteomic analysis of house dust mite antigens reveals distinct classes of dominant T cell antigens according to function and serological reactivity. PMID:27684489
Current tools for predicting cancer-specific T cell immunity. PMID:27622028
A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis. PMID:27506766
HLA-DRB1 Alleles Are Associated With Different Magnitudes of Dengue Virus-Specific CD4+ T-Cell Responses. PMID:27443615
Analysis of Major Histocompatibility Complex-Bound HIV Peptides Identified from Various Cell Types Reveals Common Nested Peptides and Novel T Cell Responses. PMID:27440904
A Quantitative Analysis of Complexity of Human Pathogen-Specific CD4 T Cell Responses in Healthy M. tuberculosis Infected South Africans. PMID:27409590
Computational genomics tools for dissecting tumour-immune cell interactions. PMID:27376489
Chemical Modification of Influenza CD8+ T-Cell Epitopes Enhances Their Immunogenicity Regardless of Immunodominance. PMID:27333291
Design and engineering of deimmunized biotherapeutics. PMID:27322891
HLAsupE: an integrated database of HLA supertype-specific epitopes to aid in the development of vaccines with broad coverage of the human population. PMID:27307005
Literature information in PubChem: associations between PubChem records and scientific articles. PMID:27293485
Expressing Redundancy among Linear-Epitope Sequence Data Based on Residue-Level Physicochemical Similarity in the Context of Antigenic Cross-Reaction. PMID:27274725
Evaluation of the immunogenicity and protective effects of a trivalent chimeric norovirus P particle immunogen displaying influenza HA2 from subtypes H1, H3 and B. PMID:27222326
Th1 versus Th2 T cell polarization by whole-cell and acellular childhood pertussis vaccines persists upon re-immunization in adolescence and adulthood. PMID:27212461
Putative virulence factors of Corynebacterium pseudotuberculosis FRC41: vaccine potential and protein expression. PMID:27184574
Dual B- and T-cell de-immunization of recombinant immunotoxin targeting mesothelin with high cytotoxic activity. PMID:27167198
FRED 2: an immunoinformatics framework for Python. PMID:27153717
The Ontology for Biomedical Investigations. PMID:27128319
The omic approach to parasitic trematode research-a review of techniques and developments within the past 5 years. PMID:27126082
A web-based resource for designing therapeutics against Ebola Virus. PMID:27113850
Analyzing the effect of peptide-HLA-binding ability on the immunogenicity of potential CD8+ and CD4+ T cell epitopes in a large dataset. PMID:27094547
Designing therapeutic cancer vaccines by mimicking viral infections. PMID:27052572
NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets. PMID:27029192
HIV Protease Inhibitor-Induced Cathepsin Modulation Alters Antigen Processing and Cross-Presentation. PMID:27009491
Promiscuous Recognition of a Trypanosoma cruzi CD8+ T Cell Epitope among HLA-A2, HLA-A24 and HLA-A1 Supertypes in Chagasic Patients. PMID:26974162
Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations. PMID:26928227
The Role of Neoantigens in Naturally Occurring and Therapeutically Induced Immune Responses to Cancer. PMID:26922999
Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients. PMID:26901407
High-Density Peptide Microarray Analysis of IgG Autoantibody Reactivities in Serum and Cerebrospinal Fluid of Multiple Sclerosis Patients. PMID:26831522
pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens. PMID:26825632
The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference. PMID:26783342
An ontology for major histocompatibility restriction. PMID:26759709
Reproducibility and conflicts in immune epitope data. PMID:26678806
DockTope: a Web-based tool for automated pMHC-I modelling. PMID:26674250
Population tailored modification of tuberculosis specific interferon-gamma release assay. PMID:26632326
Immune Responses in Acute and Convalescent Patients with Mild, Moderate and Severe Disease during the 2009 Influenza Pandemic in Norway. PMID:26606759
EPIPOX: Immunoinformatic Characterization of the Shared T-Cell Epitome between Variola Virus and Related Pathogenic Orthopoxviruses. PMID:26605344
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263
Immunoinformatics and epitope prediction in the age of genomic medicine. PMID:26589500
Automatic Generation of Validated Specific Epitope Sets. PMID:26568965
SATPdb: a database of structurally annotated therapeutic peptides. PMID:26527728
Gapped sequence alignment using artificial neural networks: application to the MHC class I system. PMID:26515819
BDB: biopanning data bank. PMID:26503249
Rapid isolation of dengue-neutralizing antibodies from single cell-sorted human antigen-specific memory B-cell cultures. PMID:26491897
Elimination of murine and human T-cell epitopes in recombinant immunotoxin eliminates neutralizing and anti-drug antibodies in vivo. PMID:26477977
Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification. PMID:26416257
Common Amino Acid Subsequences in a Universal Proteome--Relevance for Food Science. PMID:26340620
Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages. PMID:26311880
Mechanism of Binding to Ebola Virus Glycoprotein by the ZMapp, ZMAb, and MB-003 Cocktail Antibodies. PMID:26311869
Tumor neoantigens: building a framework for personalized cancer immunotherapy. PMID:26258412
Epitopemap: a web application for integrated whole proteome epitope prediction. PMID:26169908
iVAX: An integrated toolkit for the selection and optimization of antigens and the design of epitope-driven vaccines. PMID:26155959
The Disease Ontology: fostering interoperability between biological and clinical human disease-related data. PMID:26093607
Generation and Identification of Peptide-Based Monoclonal Antibodies Against Vacuolar Proton Pyrophosphatase of Toxoplasma gondii. PMID:26090597
Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes. PMID:25862607
Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy. PMID:25853550
Definition of a pool of epitopes that recapitulates the T cell reactivity against major house dust mite allergens. PMID:25652035
The immune epitope database 2.0 PubMed citations: 302.

302 articles citing: The immune epitope database 2.0

Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods. PMID:35729277
BepFAMN: A Method for Linear B-Cell Epitope Predictions Based on Fuzzy-ARTMAP Artificial Neural Network. PMID:35684648
In silico epitope-based vaccine design against influenza a neuraminidase protein: Computational analysis established on B- and T-cell epitope predictions. PMID:35574284
HPVMD-C: a disease-based mutation database of human papillomavirus in China. PMID:35348640
Design of Monovalent and Chimeric Tetravalent Dengue Vaccine Using an Immunoinformatics Approach. PMID:34602919
T Cell Specificity: A Great Challenge in Chagas Disease. PMID:34267750
EpitopeVec: Linear Epitope Prediction Using Deep Protein Sequence Embeddings. PMID:34180989
Linear B-Cell Epitope Prediction for In Silico Vaccine Design: A Performance Review of Methods Available via Command-Line Interface. PMID:33809918
Advanced strategies for development of vaccines against human bacterial pathogens. PMID:33748926
The analysis on the human protein domain targets and host-like interacting motifs for the MERS-CoV and SARS-CoV/CoV-2 infers the molecular mimicry of coronavirus. PMID:33596252
Peptides-based vaccine against SARS-nCoV-2 antigenic fragmented synthetic epitopes recognized by T cell and β-cell initiation of specific antibodies to fight the infection. PMID:33552630
Antigen identification for HLA class I- and HLA class II-restricted T cell receptors using cytokine-capturing antigen-presenting cells. PMID:33483338
Immuno-informatics approach for B-cell and T-cell epitope based peptide vaccine design against novel COVID-19 virus. PMID:33478787
Norovirus-Specific CD8+ T Cell Responses in Human Blood and Tissues. PMID:33444817
A Highly Conserved Epitope (RNNQIPQDF) of Porcine teschovirus Induced a Group-Specific Antiserum: A Bioinformatics-Predicted Model with Pan-PTV Potential. PMID:33138189
Exploring the out of sight antigens of SARS-CoV-2 to design a candidate multi-epitope vaccine by utilizing immunoinformatics approaches. PMID:33082015
A bio-safe multiple antigenic peptide (MAP) enzyme-linked immunoassay for the detection of antibodies to infectious bronchitis virus in chickens. PMID:32999814
Generation of SARS-CoV-2 S1 Spike Glycoprotein Putative Antigenic Epitopes in Vitro by Intracellular Aminopeptidases. PMID:32931291
Unique genomic and neoepitope landscapes across tumors: a study across time, tissues, and space within a single lynch syndrome patient. PMID:32699259
A Peptide Link Between Human Cytomegalovirus Infection, Neuronal Migration, and Psychosis. PMID:32457660
Epitopes for a 2019-nCoV vaccine. PMID:32094505
pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens. PMID:31907209
The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook. PMID:31761977
Computational approaches to therapeutic antibody design: established methods and emerging trends. PMID:31626279
In silico analysis as a strategy to identify candidate epitopes with human IgG reactivity to study Porphyromonas gingivalis virulence factors. PMID:30859419
The neoepitope landscape of breast cancer: implications for immunotherapy. PMID:30832597
In silico design of a triple-negative breast cancer vaccine by targeting cancer testis antigens. PMID:30788259
Fine-Specificity Epitope Analysis Identifies Contact Points on Ricin Toxin Recognized by Protective Monoclonal Antibodies. PMID:30766971
Weighted lambda superstrings applied to vaccine design. PMID:30735507
BioReader: a text mining tool for performing classification of biomedical literature. PMID:30717659
Clinical, immunological and bacteriological characteristics of H7N9 patients nosocomially co-infected by Acinetobacter Baumannii: a case control study. PMID:30551738
The Utility of Supertype Clustering in Prediction for Class II MHC-Peptide Binding. PMID:30463372
A real-time PCR assay for quantification of parasite burden in murine models of leishmaniasis. PMID:30430041
Identifying neoantigens for use in immunotherapy. PMID:30167844
Combination of M2e peptide with stalk HA epitopes of influenza A virus enhances protective properties of recombinant vaccine. PMID:30138320
The association of genomic lesions and PD-1/PD-L1 expression in resected triple-negative breast cancers. PMID:29996881
Proteome-wide analysis of human motif-domain interactions mapped on influenza a virus. PMID:29940841
Influence of the Linking Order of Fragments of HA2 and M2e of the influenza A Virus to Flagellin on the Properties of Recombinant Proteins. PMID:29713522
Flagellin-fused protein targeting M2e and HA2 induces potent humoral and T-cell responses and protects mice against various influenza viruses a subtypes. PMID:29631629
Novel Plasmodium antigens identified via genome-based antibody screen induce protection associated with polyfunctional T cell responses. PMID:29118376
Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data. PMID:29115832
The neoepitope landscape in pediatric cancers. PMID:28854978
Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection. PMID:28835708
In silico analysis to identify vaccine candidates common to multiple serotypes of Shigella and evaluation of their immunogenicity. PMID:28767653
A computational pipeline to generate MHC binding motifs. PMID:28747991
Genotype-specific acquisition, evolution and adaptation of characteristic mutations in hepatitis E virus. PMID:28727933
The Immune Epitope Database: How Data Are Entered and Retrieved. PMID:28634590
Epitope mapping and kinetics of CD4 T cell immunity to pneumonia virus of mice in the C57BL/6 strain. PMID:28615708
In silico and cell-based analyses reveal strong divergence between prediction and observation of T-cell-recognized tumor antigen T-cell epitopes. PMID:28536262
Citrullination only infrequently impacts peptide binding to HLA class II MHC. PMID:28481943
From Toxoplasmosis to Schizophrenia via NMDA Dysfunction: Peptide Overlap between Toxoplasma gondii and N-Methyl-d-Aspartate Receptors As a Potential Mechanistic Link. PMID:28360866
Bioinformatic prediction of the epitopes of Echinococcus granulosus antigen 5. PMID:28357070
Computational prediction of immunodominant antigenic regions & potential protective epitopes for dengue vaccination. PMID:28256468
A Mutation Identified in Neonatal Microcephaly Destabilizes Zika Virus NS1 Assembly in Vitro. PMID:28198446
HPV and systemic lupus erythematosus: a mosaic of potential crossreactions. PMID:28111707
A Bioinformatics Practicum to Develop Student Understanding of Immunological Rejection of Protein Drugs. PMID:28090096
Polymorphism of 41 kD Flagellin Gene and Its Human B-Cell Epitope in Borrelia burgdorferi Strains of China. PMID:28042565
Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade. PMID:27956380
Development of a Peptide ELISA for the Diagnosis of Aleutian Mink Disease. PMID:27802320
Identifying Novel B Cell Epitopes within Toxoplasma gondii GRA6. PMID:27658594
Long-term adaptation of the influenza A virus by escaping cytotoxic T-cell recognition. PMID:27629812
sNebula, a network-based algorithm to predict binding between human leukocyte antigens and peptides. PMID:27558848
In-silico discovery of cancer-specific peptide-HLA complexes for targeted therapy. PMID:27439771
A Fusion Protein Based on the Second Subunit of Hemagglutinin of Influenza A/H2N2 Viruses Provides Cross Immunity. PMID:27437146
Do HLA class II genes protect against pulmonary tuberculosis? A systematic review and meta-analysis. PMID:27412154
In silico proposition to predict cluster of B- and T-cell epitopes for the usefulness of vaccine design from invasive, virulent and membrane associated proteins of C. jejuni. PMID:27376537
Ebolavirus evolves in human to minimize the detection by immune cells by accumulating adaptive mutations. PMID:27366764
Rational Design of Peptide Vaccines Against Multiple Types of Human Papillomavirus. PMID:27279731
HLA class I molecular variation and peptide-binding properties suggest a model of joint divergent asymmetric selection. PMID:27233953
Scratching the Surface: Resurfacing Proteins to Endow New Properties and Function. PMID:27203375
Integrated sequence and immunology filovirus database at Los Alamos. PMID:27103629
A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. PMID:27096425
Analyzing the effect of peptide-HLA-binding ability on the immunogenicity of potential CD8+ and CD4+ T cell epitopes in a large dataset. PMID:27094547
Identification of HLA-A*11:01-restricted Mycobacterium tuberculosis CD8(+) T cell epitopes. PMID:27072810
Immunogenicity of a chimeric Plasmodium falciparum merozoite surface protein vaccine in Aotus monkeys. PMID:26975721
Two highly similar LAEDDTNAQKT and LTDKIGTEI epitopes in G glycoprotein may be useful for effective epitope based vaccine design against pathogenic Henipavirus. PMID:26970211
Conserved antigenic sites between MERS-CoV and Bat-coronavirus are revealed through sequence analysis. PMID:26962326
Autoimmune Responses to Soluble Aggregates of Amyloidogenic Proteins Involved in Neurodegenerative Diseases: Overlapping Aggregation Prone and Autoimmunogenic regions. PMID:26924748
CD4+ T-cell epitope prediction using antigen processing constraints. PMID:26891811
Extensive CD4 and CD8 T Cell Cross-Reactivity between Alphaherpesviruses. PMID:26810224
T Cell Epitope Peptide Therapy for Allergic Diseases. PMID:26768622
Classification epitopes in groups based on their protein family. PMID:26696329
Prediction of linear B-cell epitopes of hepatitis C virus for vaccine development. PMID:26680271
Characterization of Immunodominant BK Polyomavirus 9mer Epitope T Cell Responses. PMID:26663765
M. tuberculosis T Cell Epitope Analysis Reveals Paucity of Antigenic Variation and Identifies Rare Variable TB Antigens. PMID:26607161
Review on the identification and role of Toxoplasma gondii antigenic epitopes. PMID:26581372
HLA Preferences for Conserved Epitopes: A Potential Mechanism for Hepatitis C Clearance. PMID:26579127
Automatic Generation of Validated Specific Epitope Sets. PMID:26568965
Applying the Concept of Peptide Uniqueness to Anti-Polio Vaccination. PMID:26568962
Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity. PMID:26513360
Machine Learning Methods for Predicting HLA-Peptide Binding Activity. PMID:26512199
FluKB: A Knowledge-Based System for Influenza Vaccine Target Discovery and Analysis of the Immunological Properties of Influenza Viruses. PMID:26504853
Sequence conservation analysis and in silico human leukocyte antigen-peptide binding predictions for the Mtb72F and M72 tuberculosis candidate vaccine antigens. PMID:26493839
Understanding and predicting binding between human leukocyte antigens (HLAs) and peptides by network analysis. PMID:26424483
Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo. PMID:26395770
EBV-Associated Cancer and Autoimmunity: Searching for Therapies. PMID:26344947
Inntags: small self-structured epitopes for innocuous protein tagging. PMID:26322837
The Carboxy Terminus of the Ligand Peptide Determines the Stability of the MHC Class I Molecule H-2Kb: A Combined Molecular Dynamics and Experimental Study. PMID:26270965
Sequence- and Structure-Based Immunoreactive Epitope Discovery for Burkholderia pseudomallei Flagellin. PMID:26222657
Serum reactome induced by Bordetella pertussis infection and Pertussis vaccines: qualitative differences in serum antibody recognition patterns revealed by peptide microarray analysis. PMID:26129684
Viral immunology. Comprehensive serological profiling of human populations using a synthetic human virome. PMID:26045439
Zooming into the binding groove of HLA molecules: which positions and which substitutions change peptide binding most? PMID:26040913
Accurate prediction of immunogenic T-cell epitopes from epitope sequences using the genetic algorithm-based ensemble learning. PMID:26020952
Geometric Constraints Dominate the Antigenic Evolution of Influenza H3N2 Hemagglutinin. PMID:26020774
Progress and challenges in predicting protein interfaces. PMID:25971595
Identification of Novel Potential Vaccine Candidates against Tuberculosis Based on Reverse Vaccinology. PMID:25961021
Prediction of CD8+ Epitopes in Leishmania braziliensis Proteins Using EPIBOT: In Silico Search and In Vivo Validation. PMID:25905908
The therapeutic promise of disrupting the PD-1/PD-L1 immune checkpoint in cancer: unleashing the CD8 T cell mediated anti-tumor activity results in significant, unprecedented clinical efficacy in various solid tumors. PMID:25901287
Immunoregulatory T cell epitope peptides: the new frontier in allergy therapy. PMID:25900315
General Approach for Tetramer-Based Identification of Autoantigen-Reactive B Cells: Characterization of La- and snRNP-Reactive B Cells in Autoimmune BXD2 Mice. PMID:25888644
Identification of novel Mycobacterium tuberculosis CD4 T-cell antigens via high throughput proteome screening. PMID:25857935
TCR contact residue hydrophobicity is a hallmark of immunogenic CD8+ T cell epitopes. PMID:25831525
Zoster Vaccination Increases the Breadth of CD4+ T Cells Responsive to Varicella Zoster Virus. PMID:25784732
Molecular docking to identify associations between drugs and class I human leukocyte antigens for predicting idiosyncratic drug reactions. PMID:25747444
Recombinant NAD-dependent SIR-2 protein of Leishmania donovani: immunobiochemical characterization as a potential vaccine against visceral leishmaniasis. PMID:25745863
Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans. PMID:25741011
Automated benchmarking of peptide-MHC class I binding predictions. PMID:25717196
EpiToolKit--a web-based workbench for vaccine design. PMID:25712691
A Highly Conserved GEQYQQLR Epitope Has Been Identified in the Nucleoprotein of Ebola Virus by Using an In Silico Approach. PMID:25709646
Deciphering complex patterns of class-I HLA-peptide cross-reactivity via hierarchical grouping. PMID:25708537
Conservancy of mAb Epitopes in Ebolavirus Glycoproteins of Previous and 2014 Outbreaks. PMID:25642381
Immunogenic peptide discovery in cancer genomes. PMID:25588790
FLAVIdB: A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology. PMID:25544857
Dipeptides catalyze rapid peptide exchange on MHC class I molecules. PMID:25535340
EPMLR: sequence-based linear B-cell epitope prediction method using multiple linear regression. PMID:25523327
Association of HLA-DRB1 with Sarcoidosis Susceptibility and Progression in African Americans. PMID:25506722
T cell epitope mapping of the e-protein of West Nile virus in BALB/c mice. PMID:25506689
Grouping of large populations into few CTL immune 'response-types' from influenza H1N1 genome analysis. PMID:25505972
In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases. PMID:25486901
The use of signal peptide domains as vaccine candidates. PMID:25483491
Role of peptide processing predictions in T cell epitope identification: contribution of different prediction programs. PMID:25475908
Varicella-zoster virus-derived major histocompatibility complex class I-restricted peptide affinity is a determining factor in the HLA risk profile for the development of postherpetic neuralgia. PMID:25355886
A comparison of two methods for T cell epitope mapping: "cell free" in vitro versus immunoinformatics. PMID:25346774
Analyzing and identifying novel B cell epitopes within Toxoplasma gondii GRA4. PMID:25301141
The immune epitope database (IEDB) 3.0. PMID:25300482
Navigating diabetes-related immune epitope data: resources and tools provided by the Immune Epitope Database (IEDB). PMID:25140192
Designing peptide-based HIV vaccine for Chinese. PMID:25136573
A distinct immunogenic region of glutamic acid decarboxylase 65 is naturally processed and presented by human islet cells to cytotoxic CD8 T cells. PMID:25112375
Coinfection. Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation. PMID:25082704
Immunodominance changes as a function of the infecting dengue virus serotype and primary versus secondary infection. PMID:25056881
Big data analytics in immunology: a knowledge-based approach. PMID:25045677
T cell antigen discovery using soluble vaccinia proteome reveals recognition of antigens with both virion and nonvirion association. PMID:25024392
Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions. PMID:25017736
HLA-DRB1*07:01 is associated with a higher risk of asparaginase allergies. PMID:24970932
Conservation of T cell epitopes between seasonal influenza viruses and the novel influenza A H7N9 virus. PMID:24950786
A human-specific allelic group of the MHC DRB1 gene in primates. PMID:24928070
Titrating T-cell epitopes within self-assembled vaccines optimizes CD4+ helper T cell and antibody outputs. PMID:24923735
Comprehensive analysis of contributions from protein conformational stability and major histocompatibility complex class II-peptide binding affinity to CD4+ epitope immunogenicity in HIV-1 envelope glycoprotein. PMID:24920818
Ontology-supported research on vaccine efficacy, safety and integrative biological networks. PMID:24909153
The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis. PMID:24886930
A highly conserved WDYPKCDRA epitope in the RNA directed RNA polymerase of human coronaviruses can be used as epitope-based universal vaccine design. PMID:24884408
Low level of HIV-1 evolution after transmission from mother to child. PMID:24866155
NetTepi: an integrated method for the prediction of T cell epitopes. PMID:24863339
A high-throughput shotgun mutagenesis approach to mapping B-cell antibody epitopes. PMID:24854488
Removing T-cell epitopes with computational protein design. PMID:24843166
Epistatically interacting substitutions are enriched during adaptive protein evolution. PMID:24811236
Nonsynonymous substitution rate heterogeneity in the peptide-binding region among different HLA-DRB1 lineages in humans. PMID:24793785
Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival. PMID:24782321
Influenza virus infection elicits protective antibodies and T cells specific for host cell antigens also expressed as tumor-associated antigens: a new view of cancer immunosurveillance. PMID:24778322
Statistical linkage analysis of substitutions in patient-derived sequences of genotype 1a hepatitis C virus nonstructural protein 3 exposes targets for immunogen design. PMID:24760894
Engaging adaptive immunity with biomaterials. PMID:24729870
CD8+ T Lymphocyte Epitopes From The Herpes Simplex Virus Type 2 ICP27, VP22 and VP13/14 Proteins To Facilitate Vaccine Design And Characterization. PMID:24709642
HPVdb: a data mining system for knowledge discovery in human papillomavirus with applications in T cell immunology and vaccinology. PMID:24705205
Preexisting CD4+ T-cell immunity in human population to avian influenza H7N9 virus: whole proteome-wide immunoinformatics analyses. PMID:24609014
Integrative immunoinformatics for Mycobacterial diseases in R platform. PMID:24592289
Genome-wide structural modelling of TCR-pMHC interactions. PMID:24564684
Literature classification for semi-automated updating of biological knowledgebases. PMID:24564403
MHC2SKpan: a novel kernel based approach for pan-specific MHC class II peptide binding prediction. PMID:24564280
Flavivirus NS1 structures reveal surfaces for associations with membranes and the immune system. PMID:24505133
Prediction of IL4 inducing peptides. PMID:24489573
A heterobivalent ligand inhibits mast cell degranulation via selective inhibition of allergen-IgE interactions in vivo. PMID:24489096
Clustering HLA class I superfamilies using structural interaction patterns. PMID:24475163
Characterization of glycolytic enzymes--rAldolase and rEnolase of Leishmania donovani, identified as Th1 stimulatory proteins, for their immunogenicity and immunoprophylactic efficacies against experimental visceral leishmaniasis. PMID:24475071
Improved pan-specific MHC class I peptide-binding predictions using a novel representation of the MHC-binding cleft environment. PMID:24447175
Designing of interferon-gamma inducing MHC class-II binders. PMID:24304645
A novel vaccine p846 encoding Rv3615c, Mtb10.4, and Rv2660c elicits robust immune response and alleviates lung injury induced by Mycobacterium infection. PMID:24280763
Genetic mutations in influenza H3N2 viruses from a 2012 epidemic in Southern China. PMID:24279698
Localization of non-linear neutralizing B cell epitopes on ricin toxin's enzymatic subunit (RTA). PMID:24269767
Characterizing monkeypox virus specific CD8+ T cell epitopes in rhesus macaques. PMID:24210113
Properties of MHC class I presented peptides that enhance immunogenicity. PMID:24204222
HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity. PMID:24190657
Sequence analysis of T-cell repertoires in health and disease. PMID:24172704
Loss of immune escape mutations during persistent HCV infection in pregnancy enhances replication of vertically transmitted viruses. PMID:24162814
Structure-based design of altered MHC class II-restricted peptide ligands with heterogeneous immunogenicity. PMID:24108701
Immunoinformatic docking approach for the analysis of KIR3DL1/HLA-B interaction. PMID:23984333
Bioinformatics resources and tools for conformational B-cell epitope prediction. PMID:23970944
Local CD4 and CD8 T-cell reactivity to HSV-1 antigens documents broad viral protein expression and immune competence in latently infected human trigeminal ganglia. PMID:23966859
A fast Peptide Match service for UniProt Knowledgebase. PMID:23958731
Exosomes carrying mycobacterial antigens can protect mice against Mycobacterium tuberculosis infection. PMID:23943377
NetMHCstab - predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery. PMID:23927693
Simultaneous TCR and CD244 signals induce dynamic downmodulation of CD244 on human antiviral T cells. PMID:23913963
NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ. PMID:23900783
A chimeric Plasmodium falciparum merozoite surface protein vaccine induces high titers of parasite growth inhibitory antibodies. PMID:23897613
Peptide-based vaccinology: experimental and computational approaches to target hypervariable viruses through the fine characterization of protective epitopes recognized by monoclonal antibodies and the identification of T-cell-activating peptides. PMID:23878584
Immunization with apical membrane antigen 1 confers sterile infection-blocking immunity against Plasmodium sporozoite challenge in a rodent model. PMID:23836827
Integrating peptides' sequence and energy of contact residues information improves prediction of peptide and HLA-I binding with unknown alleles. PMID:23815611
Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions. PMID:23815072
MHCcluster, a method for functional clustering of MHC molecules. PMID:23775223
Scrutinizing MHC-I binding peptides and their limits of variation. PMID:23754940
Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization. PMID:23748502
Identification of minimal human MHC-restricted CD8+ T-cell epitopes within the Plasmodium falciparum circumsporozoite protein (CSP). PMID:23738590
Query enhancement through the practical application of ontology: the IEDB and OBI. PMID:23734660
Ara h 1 CD4+ T cell epitope-based peptides: candidates for a peanut allergy therapeutic. PMID:23711131
Cataloging the biomedical world of pain through semi-automated curation of molecular interactions. PMID:23707966
Stability-mediated epistasis constrains the evolution of an influenza protein. PMID:23682315
Identification of targets of CD8⁺ T cell responses to malaria liver stages by genome-wide epitope profiling. PMID:23675294
Improved method for linear B-cell epitope prediction using antigen's primary sequence. PMID:23667458
A novel transport mechanism for MOMP in Chlamydophila pneumoniae and its putative role in immune-therapy. PMID:23637791
HCV Envelope protein 2 sequence comparison of Pakistani isolate and In-silico prediction of conserved epitopes for vaccine development. PMID:23631455
Persistent enteric murine norovirus infection is associated with functionally suboptimal virus-specific CD8 T cell responses. PMID:23596300
VaccImm: simulating peptide vaccination in cancer therapy. PMID:23586423
A broad profile of co-dominant epitopes shapes the peripheral Mycobacterium tuberculosis specific CD8+ T-cell immune response in South African patients with active tuberculosis. PMID:23555576
Detection of site-specific positive Darwinian selection on pandemic influenza A/H1N1 virus genome: integrative approaches. PMID:23529677
The mucosal adjuvant cholera toxin B instructs non-mucosal dendritic cells to promote IgA production via retinoic acid and TGF-β. PMID:23527272
The human leukocyte antigen-presented ligandome of B lymphocytes. PMID:23481700
Predictor for the effect of amino acid composition on CD4+ T cell epitopes preprocessing. PMID:23481624
Highly conserved antigenic epitope regions of hemagglutinin and neuraminidase genes between 2009 H1N1 and seasonal H1N1 influenza: vaccine considerations. PMID:23433453
PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity. PMID:23409948
A strategy to determine HLA class II restriction broadly covering the DR, DP, and DQ allelic variants most commonly expressed in the general population. PMID:23392739
Measurement of MHC/peptide interactions by gel filtration or monoclonal antibody capture. PMID:23392640
Positional bias of MHC class I restricted T-cell epitopes in viral antigens is likely due to a bias in conservation. PMID:23357871
T cell epitope mapping of JC polyoma virus-encoded proteome reveals reduced T cell responses in HLA-DRB1*04:01+ donors. PMID:23302880
Characterization of novel multiantigenic vaccine candidates with pan-HLA coverage against Mycobacterium tuberculosis. PMID:23283639
Diagnostic peptide discovery: prioritization of pathogen diagnostic markers using multiple features. PMID:23272069
Sequence-based in silico analysis of well studied hepatitis C virus epitopes and their variants in other genotypes (particularly genotype 5a) against South African human leukocyte antigen backgrounds. PMID:23227878
An assessment on epitope prediction methods for protozoa genomes. PMID:23170965
Vaccines: from empirical development to rational design. PMID:23144616
SVMTriP: a method to predict antigenic epitopes using support vector machine to integrate tri-peptide similarity and propensity. PMID:22984622
Autoantibodies against the signal peptide domain of MUC1 in patients with multiple myeloma: Implications for disease diagnosis and prognosis. PMID:22970023
Consortium biology in immunology: the perspective from the Immunological Genome Project. PMID:22955842
B-Pred, a structure based B-cell epitopes prediction server. PMID:22888263
Challenges and opportunities in absorption, distribution, metabolism, and excretion studies of therapeutic biologics. PMID:22864668
Peptide binding to HLA-DP proteins at pH 5.0 and pH 7.0: a quantitative molecular docking study. PMID:22862845
Revealing the role of CD4(+) T cells in viral immunity. PMID:22851641
In silico study of rotavirus VP7 surface accessible conserved regions for antiviral drug/vaccine design. PMID:22844409
T cell responses to known allergen proteins are differently polarized and account for a variable fraction of total response to allergen extracts. PMID:22786768
Structural analysis of B-cell epitopes in antibody:protein complexes. PMID:22784991
The immune epitope database: a historical retrospective of the first decade. PMID:22681406
Abacavir induces loading of novel self-peptides into HLA-B*57: 01: an autoimmune model for HLA-associated drug hypersensitivity. PMID:22617051
Conservation analysis of dengue virus T-cell epitope-based vaccine candidates using Peptide block entropy. PMID:22566858
Comparing the similarity of different groups of bacteria to the human proteome. PMID:22558081
Detection of an autoreactive T-cell population within the polyclonal repertoire that undergoes distinct autoimmune regulator (Aire)-mediated selection. PMID:22552229
PolysacDB: a database of microbial polysaccharide antigens and their antibodies. PMID:22509333
Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire. PMID:22396638
TEPITOPEpan: extending TEPITOPE for peptide binding prediction covering over 700 HLA-DR molecules. PMID:22383964
Pre-clinical evaluation of a replication-competent recombinant adenovirus serotype 4 vaccine expressing influenza H5 hemagglutinin. PMID:22363572
Human CD4+ T cell response to human herpesvirus 6. PMID:22357271
Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. PMID:22260278
Cross-presentation and genome-wide screening reveal candidate T cells antigens for a herpes simplex virus type 1 vaccine. PMID:22214845
GuiTope: an application for mapping random-sequence peptides to protein sequences. PMID:22214541
DRB1*12:01 presents a unique subset of epitopes by preferring aromatics in pocket 9. PMID:22196942
Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation. PMID:22182279
Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy? PMID:22149708
Immunity to ricin: fundamental insights into toxin-antibody interactions. PMID:22113742
Disease Ontology: a backbone for disease semantic integration. PMID:22080554
NetMHCcons: a consensus method for the major histocompatibility complex class I predictions. PMID:22009319
ViPR: an open bioinformatics database and analysis resource for virology research. PMID:22006842
Representation of protein 3D structures in spherical (ρ, ϕ, θ) coordinates and two of its potential applications. PMID:21956738
The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation. PMID:21952136
Insights into HLA-restricted T cell responses in a novel mouse model of dengue virus infection point toward new implications for vaccine design. PMID:21918184
HLA-DP2 binding prediction by molecular dynamics simulations. PMID:21898654
Prediction of peptide reactivity with human IVIg through a knowledge-based approach. PMID:21887285
Computationally predicted IgE epitopes of walnut allergens contribute to cross-reactivity with peanuts. PMID:21883278
A broadly applicable approach to T cell epitope identification: application to improving tumor associated epitopes and identifying epitopes in complex pathogens. PMID:21872603
Engineering T cells specific for a dominant severe acute respiratory syndrome coronavirus CD8 T cell epitope. PMID:21813600
Comparative genomics of Esx genes from clinical isolates of Mycobacterium tuberculosis provides evidence for gene conversion and epitope variation. PMID:21807910
Dana-Farber repository for machine learning in immunology. PMID:21782820
Genomic expression libraries for the identification of cross-reactive orthopoxvirus antigens. PMID:21779357
Emerging vaccine informatics. PMID:21772787
Peptide binding prediction for the human class II MHC allele HLA-DP2: a molecular docking approach. PMID:21752305
HLA class I allele promiscuity revisited. PMID:21695550
Determinants of antigenicity and specificity in immune response for protein sequences. PMID:21693021
Analysis of antigenically important residues in human influenza A virus in terms of B-cell epitopes. PMID:21680505
PeptX: using genetic algorithms to optimize peptides for MHC binding. PMID:21679477
PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes. PMID:21666259
Whole-genome immunoinformatic analysis of F. tularensis: predicted CTL epitopes clustered in hotspots are prone to elicit a T-cell response. PMID:21625462
Graphical representation and mathematical characterization of protein sequences and applications to viral proteins. PMID:21570664
Tapasin discriminates peptide-human leukocyte antigen-A*02:01 complexes formed with natural ligands. PMID:21518758
Coupling of aggregation and immunogenicity in biotherapeutics: T- and B-cell immune epitopes may contain aggregation-prone regions. PMID:21437790
Constrained pattern of viral evolution in acute and early HCV infection limits viral plasticity. PMID:21347433
A computationally optimized broadly reactive antigen (COBRA) based H5N1 VLP vaccine elicits broadly reactive antibodies in mice and ferrets. PMID:21320540
Theoretical modeling techniques and their impact on tumor immunology. PMID:21234354
A generic approach to evaluate how B-cell epitopes are surface-exposed on protein structures. PMID:21111484
Peptide binding predictions for HLA DR, DP and DQ molecules. PMID:21092157
Human leukocyte antigens A*3001 and A*3002 show distinct peptide-binding patterns of the Mycobacterium tuberculosis protein TB10.4: consequences for immune recognition. PMID:21084459
NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure. PMID:21073747
State of the art and challenges in sequence based T-cell epitope prediction. PMID:21067545
Computer aided selection of candidate vaccine antigens. PMID:21067543
Prediction of epitopes using neural network based methods. PMID:21047511
Applications for T-cell epitope queries and tools in the Immune Epitope Database and Analysis Resource. PMID:21047510
IEDB-3D: structural data within the immune epitope database. PMID:21030437
An Allergen Portrait Gallery: Representative Structures and an Overview of IgE Binding Surfaces. PMID:20981266
Identification of conformational B-cell Epitopes in an antigen from its primary sequence. PMID:20961417
Protegen: a web-based protective antigen database and analysis system. PMID:20959289
Molecular modeling of class I and II alleles of the major histocompatibility complex in Salmo salar. PMID:20936494
CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies. PMID:20663186
Repertoire of HLA-DR1-restricted CD4 T-cell responses to capsular Caf1 antigen of Yersinia pestis in human leukocyte antigen transgenic mice. PMID:20660611
High throughput T epitope mapping and vaccine development. PMID:20617148
MHC I stabilizing potential of computer-designed octapeptides. PMID:20508831
Controlling influenza by cytotoxic T-cells: calling for help from destroyers. PMID:20508820
Relics of selection in the mycobacterial genome. PMID:20502489
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. PMID:19965766
The immune epitope database and analysis resource: from vision to blueprint PubMed citations: 186.

186 articles citing: The immune epitope database and analysis resource: from vision to blueprint

Compilation of parasitic immunogenic proteins from 30 years of published research using machine learning and natural language processing. PMID:35725870
Vaccines and Immunoinformatics for Vaccine Design. PMID:35594022
Towards the prediction of non-peptidic epitopes. PMID:35180214
Immunoinformatics prediction of potential immunodominant epitopes from human coronaviruses and association with autoimmunity. PMID:35006282
Engineering of Cytolethal Distending Toxin B by Its Reducing Immunogenicity and Maintaining Stability as a New Drug Candidate for Tumor Therapy; an In Silico Study. PMID:34822569
Mechanisms of Immunotoxicity: Stressors and Evaluators. PMID:34361007
Allele-Specific Thresholds of Eluted Ligands for T-Cell Epitope Prediction. PMID:34303001
Immuno-informatics design of a multimeric epitope peptide based vaccine targeting SARS-CoV-2 spike glycoprotein. PMID:33730022
Deimmunization of protein therapeutics - Recent advances in experimental and computational epitope prediction and deletion. PMID:33425259
T and B cell Epitope analysis of SARS-CoV-2 S protein based on immunoinformatics and experimental research. PMID:33325143
Epitope-Based Potential Vaccine Candidate for Humoral and Cell-Mediated Immunity to Combat Severe Acute Respiratory Syndrome Coronavirus 2 Pandemic. PMID:33174418
Attenuated Subcomponent Vaccine Design Targeting the SARS-CoV-2 Nucleocapsid Phosphoprotein RNA Binding Domain: In Silico Analysis. PMID:32964056
Epitope-based peptide vaccines predicted against novel coronavirus disease caused by SARS-CoV-2. PMID:32621841
A behind-the-scenes tour of the IEDB curation process: an optimized process empirically integrating automation and human curation efforts. PMID:32615639
Genomic Sequencing and Analysis of Eight Camel-Derived Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Isolates in Saudi Arabia. PMID:32503352
Factors in B cell competition and immunodominance. PMID:32483855
A structured model for immune exposures. PMID:32283555
The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook. PMID:31761977
Epitope-based peptide vaccine design and target site depiction against Middle East Respiratory Syndrome Coronavirus: an immune-informatics study. PMID:31703698
A general approach for predicting protein epitopes targeted by antibody repertoires using whole proteomes. PMID:31490930
Comprehensive Review of Human Plasmodium falciparum-Specific CD8+ T Cell Epitopes. PMID:30949162
APOBEC3G Regulation of the Evolutionary Race Between Adaptive Immunity and Viral Immune Escape Is Deeply Imprinted in the HIV Genome. PMID:30687306
Synthetic biology for bioengineering virus-like particle vaccines. PMID:30597533
Subtractive proteomics to identify novel drug targets and reverse vaccinology for the development of chimeric vaccine against Acinetobacter baumannii. PMID:29899345
Analysis of viral diversity for vaccine target discovery. PMID:29322922
Novel Plasmodium antigens identified via genome-based antibody screen induce protection associated with polyfunctional T cell responses. PMID:29118376
DRREP: deep ridge regressed epitope predictor. PMID:28984193
Purification and characterization of a highly specific polyclonal antibody against human extracellular signal-regulated kinase 8 and its detection in lung cancer. PMID:28902877
Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences. PMID:28361709
Characterization of γδ T Cells from Zebrafish Provides Insights into Their Important Role in Adaptive Humoral Immunity. PMID:28119690
TepiTool: A Pipeline for Computational Prediction of T Cell Epitope Candidates. PMID:27479659
Prediction of Immunomodulatory potential of an RNA sequence for designing non-toxic siRNAs and RNA-based vaccine adjuvants. PMID:26861761
Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications. PMID:26501781
Epitope Prediction Assays Combined with Validation Assays Strongly Narrows down Putative Cytotoxic T Lymphocyte Epitopes. PMID:26343185
VaccineDA: Prediction, design and genome-wide screening of oligodeoxynucleotide-based vaccine adjuvants. PMID:26212482
Learning sequence determinants of protein:protein interaction specificity with sparse graphical models. PMID:25973864
Progress on adenovirus-vectored universal influenza vaccines. PMID:25876176
Grouping of large populations into few CTL immune 'response-types' from influenza H1N1 genome analysis. PMID:25505972
Identification and retrospective validation of T-cell epitopes in the hepatitis C virus genotype 4 proteome: an accelerated approach toward epitope-driven vaccine development. PMID:25424944
Learning Sequence Determinants of Protein:protein Interaction Specificity with Sparse Graphical Models. PMID:25414914
Prediction of epitope-based peptides for the utility of vaccine development from fusion and glycoprotein of nipah virus using in silico approach. PMID:25147564
Navigating diabetes-related immune epitope data: resources and tools provided by the Immune Epitope Database (IEDB). PMID:25140192
Measurement of Peptide Binding to MHC Class II Molecules by Fluorescence Polarization. PMID:25081912
Model for vaccine design by prediction of B-epitopes of IEDB given perturbations in peptide sequence, in vivo process, experimental techniques, and source or host organisms. PMID:24741624
A novel method to measure HLA-DM-susceptibility of peptides bound to MHC class II molecules based on peptide binding competition assay and differential IC(50) determination. PMID:24583195
Clinical implications of evolutionary patterns of homologous, full-length hepatitis B virus quasispecies in different hosts after perinatal infection. PMID:24574300
Targeting a cross-reactive Gly m 5 soy peptide as responsible for hypersensitivity reactions in a milk allergy mouse model. PMID:24416141
Alphavirus-based vaccines encoding nonstructural proteins of hepatitis C virus induce robust and protective T-cell responses. PMID:24370701
Selection of conserved epitopes from hepatitis C virus for pan-populational stimulation of T-cell responses. PMID:24348677
Large scale genome analysis shows that the epitopes for broadly cross-reactive antibodies are predominant in the pandemic 2009 influenza virus A H1N1 strain. PMID:24257096
HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity. PMID:24190657
VaccImm: simulating peptide vaccination in cancer therapy. PMID:23586423
Learning a peptide-protein binding affinity predictor with kernel ridge regression. PMID:23497081
Peptide sharing between influenza A H1N1 hemagglutinin and human axon guidance proteins. PMID:23378012
Prediction of peptides binding to MHC class I and II alleles by temporal motif mining. PMID:23368521
EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information. PMID:23176036
HLA-DM constrains epitope selection in the human CD4 T cell response to vaccinia virus by favoring the presentation of peptides with longer HLA-DM-mediated half-lives. PMID:22966084
CD8 T cell epitope distribution in viruses reveals patterns of protein biosynthesis. PMID:22952734
Early HLA-B*57-restricted CD8+ T lymphocyte responses predict HIV-1 disease progression. PMID:22811521
A human CD4+ T cell epitope in the influenza hemagglutinin is cross-reactive to influenza A virus subtypes and to influenza B virus. PMID:22718815
Comparing the similarity of different groups of bacteria to the human proteome. PMID:22558081
The utility and limitations of current Web-available algorithms to predict peptides recognized by CD4 T cells in response to pathogen infection. PMID:22467652
Research resources: curating the new eagle-i discovery system. PMID:22434835
Selfness-nonselfness in designing an anti-B19 erythrovirus vaccine. PMID:22299063
Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation. PMID:22182279
POPISK: T-cell reactivity prediction using support vector machines and string kernels. PMID:22085524
Targets for the induction of protective immunity against influenza a viruses. PMID:21994606
A broadly applicable approach to T cell epitope identification: application to improving tumor associated epitopes and identifying epitopes in complex pathogens. PMID:21872603
Development of immune-specific interaction potentials and their application in the multi-agent-system VaccImm. PMID:21858048
OETMAP: a new feature encoding scheme for MHC class I binding prediction. PMID:21805091
Dana-Farber repository for machine learning in immunology. PMID:21782820
Emerging vaccine informatics. PMID:21772787
Clustering of rare peptide segments in the HCV immunome. PMID:21487517
Towards universal structure-based prediction of class II MHC epitopes for diverse allotypes. PMID:21187956
Concept and application of a computational vaccinology workflow. PMID:21067549
Recent advances in B-cell epitope prediction methods. PMID:21067544
Computer aided selection of candidate vaccine antigens. PMID:21067543
Applications for T-cell epitope queries and tools in the Immune Epitope Database and Analysis Resource. PMID:21047510
Real-time, high-throughput measurements of peptide-MHC-I dissociation using a scintillation proximity assay. PMID:21044632
MHC-I prediction using a combination of T cell epitopes and MHC-I binding peptides. PMID:20920507
MultiRTA: a simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes. PMID:20868497
Computational analysis and modeling of cleavage by the immunoproteasome and the constitutive proteasome. PMID:20863374
Predicting MHC-II binding affinity using multiple instance regression. PMID:20855923
Divergent motifs but overlapping binding repertoires of six HLA-DQ molecules frequently expressed in the worldwide human population. PMID:20810981
Highly conserved cross-reactive CD4+ T-cell HA-epitopes of seasonal and the 2009 pandemic influenza viruses. PMID:20716156
Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development. PMID:20671958
Modeling biomedical experimental processes with OBI. PMID:20626927
Proposing low-similarity peptide vaccines against Mycobacterium tuberculosis. PMID:20625421
Bridging innate and adaptive antitumor immunity targeting glycans. PMID:20617150
NIAID workshop on Flavivirus immunity. PMID:20565288
HLA-DR1001 presents "altered-self" peptides derived from joint-associated proteins by accepting citrulline in three of its binding pockets. PMID:20533291
Major histocompatibility complex class I binding predictions as a tool in epitope discovery. PMID:20518827
MHC I stabilizing potential of computer-designed octapeptides. PMID:20508831
Controlling influenza by cytotoxic T-cells: calling for help from destroyers. PMID:20508820
Coverage of related pathogenic species by multivalent and cross-protective vaccine design: arenaviruses as a model system. PMID:20508245
IMMUNOCAT-a data management system for epitope mapping studies. PMID:20490281
Mining for the antibody-antigen interacting associations that predict the B cell epitopes. PMID:20487513
Optimization algorithms for functional deimmunization of therapeutic proteins. PMID:20380721
Identification of potential HLA class I and class II epitope precursors associated with heat shock protein 70 (HSPA). PMID:20358320
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. PMID:20214801
Design and utilization of epitope-based databases and predictive tools. PMID:20213141
HLA class I restriction as a possible driving force for Chikungunya evolution. PMID:20195467
Neutralizing epitopes of the SARS-CoV S-protein cluster independent of repertoire, antigen structure or mAb technology. PMID:20168090
Predicting MHC class I epitopes in large datasets. PMID:20163709
Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens. PMID:20143946
Five HLA-DP molecules frequently expressed in the worldwide human population share a common HLA supertypic binding specificity. PMID:20139279
Conservation and diversity of influenza A H1N1 HLA-restricted T cell epitope candidates for epitope-based vaccines. PMID:20090904
Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model. PMID:20089173
Multiple, non-conserved, internal viral ligands naturally presented by HLA-B27 in human respiratory syncytial virus-infected cells. PMID:20081153
The yellow fever virus vaccine induces a broad and polyfunctional human memory CD8+ T cell response. PMID:19933869
Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population. PMID:19918065
Evidence for a novel gene associated with human influenza A viruses. PMID:19917120
Data management: it starts at the bench. PMID:19915619
The immune epitope database 2.0. PMID:19906713
Preexisting immunity to pandemic (H1N1) 2009. PMID:19891882
Use of hepadnavirus core proteins as vaccine platforms. PMID:19863249
HLA-DR: molecular insights and vaccine design. PMID:19860674
Pathema: a clade-specific bioinformatics resource center for pathogen research. PMID:19843611
AntigenDB: an immunoinformatics database of pathogen antigens. PMID:19820110
Critical role of glycosylation in determining the length and structure of T cell epitopes. PMID:19778434
Prediction of antigenic epitopes on protein surfaces by consensus scoring. PMID:19772615
HLA class I molecules reflect an altered host proteome after influenza virus infection. PMID:19748539
Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays. PMID:19737893
Genome-wide screening of human T-cell epitopes in influenza A virus reveals a broad spectrum of CD4(+) T-cell responses to internal proteins, hemagglutinins, and neuraminidases. PMID:19524006
Two MHC class I molecules associated with elite control of immunodeficiency virus replication, Mamu-B*08 and HLA-B*2705, bind peptides with sequence similarity. PMID:19494300
Viruses selectively mutate their CD8+ T-cell epitopes--a large-scale immunomic analysis. PMID:19478014
SEPPA: a computational server for spatial epitope prediction of protein antigens. PMID:19465377
OptiTope--a web server for the selection of an optimal set of peptides for epitope-based vaccines. PMID:19420066
Conservation and variability of West Nile virus proteins. PMID:19401763
Immunoinformatics: current trends and future directions. PMID:19379830
MHCBN 4.0: A database of MHC/TAP binding peptides and T-cell epitopes. PMID:19379493
Human self-protein CD8+ T-cell epitopes are both positively and negatively selected. PMID:19291702
BEID: database for sequence-structure-function information on antigen-antibody interactions. PMID:19238231
Mathematical and computational approaches can complement experimental studies of host-pathogen interactions. PMID:19134115
HLA class I molecules consistently present internal influenza epitopes. PMID:19122146
Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research. PMID:19091022
Hepatitis C virus immune escape via exploitation of a hole in the T cell repertoire. PMID:18941234
On evaluating MHC-II binding peptide prediction methods. PMID:18813344
Memory T cells established by seasonal human influenza A infection cross-react with avian influenza A (H5N1) in healthy individuals. PMID:18802496
The peptide-binding specificity of HLA-A*3001 demonstrates membership of the HLA-A3 supertype. PMID:18769915
Conservation and variability of dengue virus proteins: implications for vaccine design. PMID:18698358
The curation guidelines of the immune epitope database and analysis resource. PMID:18688821
Comprehensive analysis of T cell epitope discovery strategies using 17DD yellow fever virus structural proteins and BALB/c (H2d) mice model. PMID:18579176
Immune epitope database analysis resource (IEDB-AR). PMID:18515843
Vaccinia peptides eluted from HLA-DR1 isolated from virus-infected cells are recognized by CD4+ T cells from a vaccinated donor. PMID:18507432
Whole genome identification of Mycobacterium tuberculosis vaccine candidates by comprehensive data mining and bioinformatic analyses. PMID:18505592
Effect of multiple genetic polymorphisms on antigen presentation and susceptibility to Mycobacterium tuberculosis infection. PMID:18443099
PRRDB: a comprehensive database of pattern-recognition receptors and their ligands. PMID:18423032
Gliadin activates HLA class I-restricted CD8+ T cells in celiac disease intestinal mucosa and induces the enterocyte apoptosis. PMID:18395083
A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PMID:18389056
Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. PMID:18366636
Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. PMID:18315850
Conditional MHC class I ligands and peptide exchange technology for the human MHC gene products HLA-A1, -A3, -A11, and -B7. PMID:18308940
Epitope discovery in West Nile virus infection: Identification and immune recognition of viral epitopes. PMID:18299564
Analysis of epitope information related to Bacillus anthracis and Clostridium botulinum. PMID:18251694
Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes. PMID:18245380
Coping with loss of perfection in the MHC class I peptide repertoire. PMID:18243675
Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries. PMID:18221540
HLA class I supertypes: a revised and updated classification. PMID:18211710
An MHC class II restriction bias in CD4 T cell responses toward I-A is altered to I-E in DM-deficient mice. PMID:18209058
Human major histocompatibility complex (MHC) class I molecules with disulfide traps secure disease-related antigenic peptides and exclude competitor peptides. PMID:18195006
The contributions of mass spectrometry to understanding of immune recognition by T lymphocytes. PMID:18167512
Modeling the adaptive immune system: predictions and simulations. PMID:18045832
Evolutionarily conserved protein sequences of influenza a viruses, avian and human, as vaccine targets. PMID:18030326
ToxoDB: an integrated Toxoplasma gondii database resource. PMID:18003657
Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. PMID:17999997
BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence. PMID:17965094
Human CD4+ T cell epitopes from vaccinia virus induced by vaccination or infection. PMID:17937498
Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. PMID:17897458
Prediction of antigenically active regions in the OmpF-like porin of Yersinia pseudotuberculosis. PMID:17695318
Automating document classification for the Immune Epitope Database. PMID:17655769
Pathogen proteins eliciting antibodies do not share epitopes with host proteins: a bioinformatics approach. PMID:17551592
Integrating epitope data into the emerging web of biomedical knowledge resources. PMID:17479127
National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. PMID:17420237
IDR knowledge base for primary immunodeficiencies. PMID:17394641
EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB). PMID:17313688
Protein sequence database for pathogenic arenaviruses. PMID:17288609
Ab and T cell epitopes of influenza A virus, knowledge and opportunities. PMID:17200302
The biocurator: connecting and enhancing scientific data. PMID:17069454
Cytotoxic T cell recognition of an HIV-1 reverse transcriptase variant peptide incorporating the K103N drug resistance mutation. PMID:16970827
From functional genomics to functional immunomics: new challenges, old problems, big rewards. PMID:16863395
Immunoinformatics comes of age. PMID:16846250
Curation of complex, context-dependent immunological data. PMID:16836764
A community resource benchmarking predictions of peptide binding to MHC-I molecules. PMID:16789818
Improved method for predicting linear B-cell epitopes. PMID:16635264
An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities. PMID:16305755
The immune epitope database: a historical retrospective of the first decade PubMed citations: 21.

21 articles citing: The immune epitope database: a historical retrospective of the first decade

Profiling Human Cytomegalovirus-Specific T Cell Responses Reveals Novel Immunogenic Open Reading Frames. PMID:34379494
SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19. PMID:34237248
Epitope prediction and identification- adaptive T cell responses in humans. PMID:33131981
The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook. PMID:31761977
Breast cancer vaccination comes to age: impacts of bioinformatics. PMID:30211082
MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection. PMID:29331515
Immunogenicity of a Multi-Epitope DNA Vaccine Encoding Epitopes from Cu-Zn Superoxide Dismutase and Open Reading Frames of Brucella abortus in Mice. PMID:28232837
Phylogenesys and homology modeling in Zika virus epidemic: food for thought. PMID:27670692
T Cell Epitope Peptide Therapy for Allergic Diseases. PMID:26768622
Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry. PMID:26628741
A novel anti-TNF scFv constructed with human antibody frameworks and antagonistic peptides. PMID:26059602
Key role of human leukocyte antigen in modulating human immunodeficiency virus progression: An overview of the possible applications. PMID:25964877
Immunoregulatory T cell epitope peptides: the new frontier in allergy therapy. PMID:25900315
A review of quantitative modeling of B cell responses to antigenic challenge. PMID:25326873
Structure-function analysis of hepatitis C virus envelope glycoproteins E1 and E2. PMID:25245635
Role of individual's T-cell immunome in controlling HIV-1 progression. PMID:24954875
Model for vaccine design by prediction of B-epitopes of IEDB given perturbations in peptide sequence, in vivo process, experimental techniques, and source or host organisms. PMID:24741624
Current approaches to fine mapping of antigen-antibody interactions. PMID:24635566
Evaluating the immunogenicity of protein drugs by applying in vitro MHC binding data and the immune epitope database and analysis resource. PMID:24222776
Bioinformatics for cancer immunology and immunotherapy. PMID:22986455
Characterization of CD4+ T cell subsets in allergy. PMID:22889592
Conservation Analysis of B-Cell Allergen Epitopes to Predict Clinical Cross-Reactivity Between Shellfish and Inhalant Invertebrate Allergens PubMed citations: 8.

8 articles citing: Conservation Analysis of B-Cell Allergen Epitopes to Predict Clinical Cross-Reactivity Between Shellfish and Inhalant Invertebrate Allergens

In Silico Prediction of Cross-Reactive Epitopes of Tropomyosin from Shrimp and Other Arthropods Involved in Allergy. PMID:35566021
Recombinant Tropomyosin from the Pacific Oyster (Crassostrea gigas) for Better Diagnosis. PMID:35159555
Aptamer-Based Fluorescent Biosensor for the Rapid and Sensitive Detection of Allergens in Food Matrices. PMID:34828878
In silico analysis of cross reactivity among phospholipases from Hymenoptera species. PMID:34046162
Novel Allergen Discovery through Comprehensive De Novo Transcriptomic Analyses of Five Shrimp Species. PMID:33375120
Emerging Food Allergy Biomarkers. PMID:32888527
Advances and novel developments in molecular allergology. PMID:32882057
Effect of structural stability on endolysosomal degradation and T-cell reactivity of major shrimp allergen tropomyosin. PMID:32436591

The immune epitope database and analysis resource: from vision to blueprint PubMed citations: 5.

http://dx.doi.org/10.1093/nar/gku938

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antibody
metasource: Fairsharing.org
version: FAIRsharing.org: IEDB; Immune Epitope Database; DOI: https://doi.org/10.25504/FAIRsharing.c886cd; Last edited: April 14, 2020, 6 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

antigen
metasource: Fairsharing.org
version: FAIRsharing.org: IEDB; Immune Epitope Database; DOI: https://doi.org/10.25504/FAIRsharing.c886cd; Last edited: April 14, 2020, 6 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

computational predictions
metasource: Fairsharing.org
version: FAIRsharing.org: IEDB; Immune Epitope Database; DOI: https://doi.org/10.25504/FAIRsharing.c886cd; Last edited: April 14, 2020, 6 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

immunity
metasource: Fairsharing.org
version: FAIRsharing.org: IEDB; Immune Epitope Database; DOI: https://doi.org/10.25504/FAIRsharing.c886cd; Last edited: April 14, 2020, 6 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

infection
metasource: Fairsharing.org
version: FAIRsharing.org: IEDB; Immune Epitope Database; DOI: https://doi.org/10.25504/FAIRsharing.c886cd; Last edited: April 14, 2020, 6 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

literature curation
metasource: Fairsharing.org
version: FAIRsharing.org: IEDB; Immune Epitope Database; DOI: https://doi.org/10.25504/FAIRsharing.c886cd; Last edited: April 14, 2020, 6 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

major histocompatibility complex
metasource: Fairsharing.org
version: FAIRsharing.org: IEDB; Immune Epitope Database; DOI: https://doi.org/10.25504/FAIRsharing.c886cd; Last edited: April 14, 2020, 6 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

t cell
metasource: Fairsharing.org
version: FAIRsharing.org: IEDB; Immune Epitope Database; DOI: https://doi.org/10.25504/FAIRsharing.c886cd; Last edited: April 14, 2020, 6 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

immunological databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

covid-19
metasource: re3data.org
version: re3data.org: Immune Epitope Database; editing status 2020-04-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3X217 last accessed: 2022-11-04

allergenes
metasource: re3data.org
version: re3data.org: Immune Epitope Database; editing status 2020-04-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3X217 last accessed: 2022-11-04

alloantigenes
metasource: re3data.org
version: re3data.org: Immune Epitope Database; editing status 2020-04-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3X217 last accessed: 2022-11-04

autoimmune diseases
metasource: re3data.org
version: re3data.org: Immune Epitope Database; editing status 2020-04-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3X217 last accessed: 2022-11-04

immune epotopes
metasource: re3data.org
version: re3data.org: Immune Epitope Database; editing status 2020-04-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3X217 last accessed: 2022-11-04

immunology
metasource: re3data.org
version: re3data.org: Immune Epitope Database; editing status 2020-04-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3X217 last accessed: 2022-11-04

infectious diseases
metasource: re3data.org
version: re3data.org: Immune Epitope Database; editing status 2020-04-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3X217 last accessed: 2022-11-04

major histocompatibility complex mhc
metasource: re3data.org
version: re3data.org: Immune Epitope Database; editing status 2020-04-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3X217 last accessed: 2022-11-04

pathogens
metasource: re3data.org
version: re3data.org: Immune Epitope Database; editing status 2020-04-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3X217 last accessed: 2022-11-04

transplant
metasource: re3data.org
version: re3data.org: Immune Epitope Database; editing status 2020-04-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3X217 last accessed: 2022-11-04

allergy, clinical immunology and immunotherapeutics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:38.998105

model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:38.998105

surgery
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:38.998105

infectious disease
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:38.998105

biomarkers
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:38.998105

antibody antigen computational predictions immunity infection literature curation major histocompatibility complex t cell immunology covid-19 allergenes alloantigenes autoimmune diseases immune epotopes immunology infectious diseases major histocompatibility complex mhc pathogens transplant allergy, clinical immunology and immunotherapeutics model organisms surgery infectious disease biomarkers

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IEDB-3D

SCEptRe

MHC Restriction Ontology

Ontology of Immune Epitopes

Virus Pathogen Database and Analysis Resource

IPD-MHC - Major Histocompatibility Complex Database

BCIpep

MaHCO

Influenza Research Database

AntigenDB

Manually Curated Database of Rice Proteins

VaximmutorDB

IPD - Immuno Polymorphism Database

Curatopes Melanoma

SDAP

PRRDB

ImMunoGeneTics Information System

OGRDB

Adaptive Immune Receptor Repertoire Data Model

HIV-1