Published in Immunogenetics on May 14, 2005
A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol (2006) 3.73
Ab and T cell epitopes of influenza A virus, knowledge and opportunities. Proc Natl Acad Sci U S A (2007) 2.67
The biocurator: connecting and enhancing scientific data. PLoS Comput Biol (2006) 2.41
ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics (2008) 2.26
Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol (2007) 2.14
Automating document classification for the Immune Epitope Database. BMC Bioinformatics (2007) 1.76
Epitome: database of structure-inferred antigenic epitopes. Nucleic Acids Res (2006) 1.70
The curation guidelines of the immune epitope database and analysis resource. Cytometry A (2008) 1.56
An analysis of the epitope knowledge related to Mycobacteria. Immunome Res (2007) 1.53
Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics (2007) 1.47
MHCBN 4.0: A database of MHC/TAP binding peptides and T-cell epitopes. BMC Res Notes (2009) 1.41
CED: a conformational epitope database. BMC Immunol (2006) 1.39
Curation of complex, context-dependent immunological data. BMC Bioinformatics (2006) 1.36
A systematic bioinformatics approach for selection of epitope-based vaccine targets. Cell Immunol (2007) 1.30
Mapping the landscape of host-pathogen coevolution: HLA class I binding and its relationship with evolutionary conservation in human and viral proteins. J Virol (2010) 1.17
An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities. Immunome Res (2005) 1.15
The utility and limitations of current Web-available algorithms to predict peptides recognized by CD4 T cells in response to pathogen infection. J Immunol (2012) 1.13
Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold. Virology (2010) 1.10
Removal of B cell epitopes as a practical approach for reducing the immunogenicity of foreign protein-based therapeutics. Adv Drug Deliv Rev (2009) 1.07
Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens. Future Microbiol (2010) 1.07
From functional genomics to functional immunomics: new challenges, old problems, big rewards. PLoS Comput Biol (2006) 0.99
The peptide-binding specificity of HLA-A*3001 demonstrates membership of the HLA-A3 supertype. Immunogenetics (2008) 0.97
Computer aided selection of candidate vaccine antigens. Immunome Res (2010) 0.95
A probabilistic meta-predictor for the MHC class II binding peptides. Immunogenetics (2007) 0.95
Bioinformatics resources and tools for conformational B-cell epitope prediction. Comput Math Methods Med (2013) 0.92
Predicting MHC class I epitopes in large datasets. BMC Bioinformatics (2010) 0.90
Secondary anchor polymorphism in the HA-1 minor histocompatibility antigen critically affects MHC stability and TCR recognition. Proc Natl Acad Sci U S A (2009) 0.89
Protein sequence database for pathogenic arenaviruses. Immunome Res (2007) 0.88
An integrated approach to epitope analysis I: Dimensional reduction, visualization and prediction of MHC binding using amino acid principal components and regression approaches. Immunome Res (2010) 0.86
HLA class I molecular variation and peptide-binding properties suggest a model of joint divergent asymmetric selection. Immunogenetics (2016) 0.79
Comparison of experimental fine-mapping to in silico prediction results of HIV-1 epitopes reveals ongoing need for mapping experiments. Immunology (2014) 0.77
Navigating diabetes-related immune epitope data: resources and tools provided by the Immune Epitope Database (IEDB). Immunome Res (2013) 0.76
Crucial epitopes of Wuchereria bancrofti abundant larval transcript recognized in natural infection. Eur J Clin Microbiol Infect Dis (2010) 0.76
Big data analytics in immunology: a knowledge-based approach. Biomed Res Int (2014) 0.75
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. In Silico Pharmacol (2016) 0.75
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. J Immunol Res (2014) 0.75
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature (1991) 13.90
Isolation of an endogenously processed immunodominant viral peptide from the class I H-2Kb molecule. Nature (1990) 6.59
Isolation and analysis of naturally processed viral peptides as recognized by cytotoxic T cells. Nature (1990) 6.23
Critical assessment of methods of protein structure prediction (CASP)-round V. Proteins (2003) 5.88
The relation between major histocompatibility complex (MHC) restriction and the capacity of Ia to bind immunogenic peptides. Science (1987) 5.32
Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism. Immunogenetics (1999) 4.88
Peptides naturally presented by MHC class I molecules. Annu Rev Immunol (1993) 4.66
The three-dimensional structure of peptide-MHC complexes. Annu Rev Immunol (1995) 4.60
The Protein Data Bank and the challenge of structural genomics. Nat Struct Biol (2000) 4.21
Danger signals: SOS to the immune system. Curr Opin Immunol (2001) 3.91
Ontology for immunogenetics: the IMGT-ONTOLOGY. Bioinformatics (1999) 3.57
Molecular interactions mediating T cell antigen recognition. Annu Rev Immunol (2001) 3.56
IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res (2005) 3.46
Promiscuous and allele-specific anchors in HLA-DR-binding peptides. Cell (1993) 3.41
Dissecting the multifactorial causes of immunodominance in class I-restricted T cell responses to viruses. Immunity (2000) 2.94
Exact prediction of a natural T cell epitope. Eur J Immunol (1991) 2.90
Type 1/Type 2 immunity in infectious diseases. Clin Infect Dis (2000) 2.79
Role of Toll-like receptors in pathogen recognition. Clin Microbiol Rev (2003) 2.59
A major role for TPPII in trimming proteasomal degradation products for MHC class I antigen presentation. Immunity (2004) 2.53
Assessment of progress over the CASP experiments. Proteins (2003) 2.43
Immunoproteasomes shape immunodominance hierarchies of antiviral CD8(+) T cells at the levels of T cell repertoire and presentation of viral antigens. J Exp Med (2001) 2.28
Chemistry of peptides associated with MHC class I and class II molecules. Curr Opin Immunol (1995) 2.15
An immunodominant conserved region within the variable domain of VlsE, the variable surface antigen of Borrelia burgdorferi. J Immunol (1999) 2.09
Structure of peptides associated with class I and class II MHC molecules. Annu Rev Immunol (1994) 2.08
Structure of a covalently stabilized complex of a human alphabeta T-cell receptor, influenza HA peptide and MHC class II molecule, HLA-DR1. EMBO J (2000) 2.00
A correlation between TCR Valpha docking on MHC and CD8 dependence: implications for T cell selection. Immunity (2003) 1.95
IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic Acids Res (2004) 1.91
Post-proteasomal antigen processing for major histocompatibility complex class I presentation. Nat Immunol (2004) 1.83
Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol (2004) 1.79
Generation of major histocompatibility complex class I antigens: functional interplay between proteasomes and TPPII. Nat Immunol (2004) 1.68
Mapping Epitope Structure and Activity: From One-Dimensional Prediction to Four-Dimensional Description of Antigenic Specificity Methods (1996) 1.63
IMGT-Choreography for immunogenetics and immunoinformatics. In Silico Biol (2005) 1.61
IMGT-ONTOLOGY for immunogenetics and immunoinformatics. In Silico Biol (2003) 1.61
Complement resistance mechanisms of streptococci. Mol Immunol (2003) 1.56
Proteolysis and class I major histocompatibility complex antigen presentation. Immunol Rev (1999) 1.47
Induction of immunity to antigens expressed by recombinant adeno-associated virus depends on the route of administration. Clin Immunol (1999) 1.45
Genetic diversity and antigenic polymorphism in Plasmodium falciparum: extensive serological cross-reactivity between allelic variants of merozoite surface protein 2. Infect Immun (2003) 1.44
The role of lysosomal proteinases in MHC class II-mediated antigen processing and presentation. Immunol Rev (1999) 1.37
Toward a definition of self: proteomic evaluation of the class I peptide repertoire. J Immunol (2004) 1.33
Uncovering subdominant cytotoxic T-lymphocyte responses in lymphocytic choriomeningitis virus-infected BALB/c mice. J Virol (1997) 1.32
Antigen degradation or presentation by MHC class I molecules via classical and non-classical pathways. Mol Immunol (2002) 1.31
Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol (2004) 1.30
Relationship between peptide selectivities of human transporters associated with antigen processing and HLA class I molecules. J Immunol (1998) 1.28
Not such a dismal science: the economics of protein synthesis, folding, degradation and antigen processing. Trends Cell Biol (2001) 1.27
Epitope mapping porcine reproductive and respiratory syndrome virus by phage display: the nsp2 fragment of the replicase polyprotein contains a cluster of B-cell epitopes. J Virol (2001) 1.22
Differential effects of flanking residues on presentation of epitopes from chimeric peptides. J Virol (1994) 1.20
Peptide binding to major histocompatibility complex molecules. Annu Rev Cell Biol (1993) 1.20
Specificity of the proteasome and the TAP transporter. Curr Opin Immunol (1999) 1.18
T cell competition for the antigen-presenting cell as a model for immunodominance in the cytotoxic T lymphocyte response against minor histocompatibility antigens. Eur J Immunol (1999) 1.17
How do we avoid developing allergy: modifications of the TH2 response from a B-cell perspective. J Allergy Clin Immunol (2004) 1.14
Synthetic vaccines: the role of adjuvants in immune targeting. Curr Med Chem (2003) 1.11
Insights into antigen processing gained by direct analysis of the naturally processed class I MHC associated peptide repertoire. Mol Immunol (2002) 1.11
Human transporters associated with antigen processing (TAPs) select epitope precursor peptides for processing in the endoplasmic reticulum and presentation to T cells. J Exp Med (1999) 1.08
Efficient priming of CD8+ memory T cells specific for a subdominant epitope following Sendai virus infection. J Immunol (1997) 1.06
Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project.". Rev Immunogenet (2000) 1.05
Overcoming T cell tolerance to the hepatitis B virus surface antigen in hepatitis B virus-transgenic mice. J Immunol (2001) 1.05
DNA vaccine strategies: candidates for immune modulation and immunization regimens. Methods (2003) 1.04
Presentation of endogenous peptide/MHC class I complexes is profoundly influenced by specific C-terminal flanking residues. J Immunol (1995) 1.03
Immunodominance of conformation-dependent B-cell epitopes of protein antigens. Biochem Biophys Res Commun (2003) 1.00
Mapping of the antibody-binding regions on botulinum neurotoxin H-chain domain 855-1296 with antitoxin antibodies from three host species. J Protein Chem (1996) 0.99
Beyond the proteasome: trimming, degradation and generation of MHC class I ligands by auxiliary proteases. Mol Immunol (2002) 0.99
Mechanisms and consequences of peptide selection by the I-Ak class II molecule. Immunol Rev (1999) 0.98
Effects of granulocyte-macrophage colony-stimulating factor and foreign helper protein as immunologic adjuvants on the T-cell response to vaccination with tyrosinase peptides. Int J Cancer (2003) 0.97
Major histocompatibility complex class I-restricted antigen processing and presentation. Tissue Antigens (2002) 0.97
Structural basis for the binding of an anti-cytochrome c antibody to its antigen: crystal structures of FabE8-cytochrome c complex to 1.8 A resolution and FabE8 to 2.26 A resolution. J Mol Biol (1998) 0.96
The function of the proteasome system in MHC class I antigen processing. Immunol Today (2000) 0.91
The 2002 Olympic Games of protein structure prediction. Protein Eng (2003) 0.91
Mapping of immunodominant B-cell epitopes and the human serum albumin-binding site in natural hepatitis B virus surface antigen of defined genosubtype. J Gen Virol (2000) 0.90
Fine specificity of autoantibodies to soluble liver antigen and liver/pancreas. Hepatology (2002) 0.89
Interactions of liposomes with cells in vitro and in vivo: opsonins and receptors. Curr Drug Metab (2001) 0.87
Structural basis of immunogenicity. Transpl Immunol (2002) 0.87
Immunogenicity assays and surrogate markers to predict vaccine efficacy. Dev Biol Stand (1998) 0.86
Results of clinical trials with an allogenic melanoma tumor cell lysate vaccine: Melacine. Semin Cancer Biol (2003) 0.86
Recognition of a novel naturally processed, A2 restricted, HCV-NS4 epitope triggers IFN-gamma release in absence of detectable cytopathicity. Hum Immunol (1998) 0.85
Immunoreactivity against linear epitopes of parvovirus B19 structural proteins. Immunodominance of the amino-terminal half of the unique region of VP1. J Med Virol (2000) 0.85
Does the autoantibody immunodominant region on thyroid peroxidase include amino acid residues 742-771? Thyroid (2001) 0.85
Quantitative analysis of peptide-MHC class II interaction. Semin Immunol (1999) 0.84
Computational vaccinology: quantitative approaches. Novartis Found Symp (2003) 0.83
Analysis of the original antigenic sin antibody response to the major outer membrane protein of Chlamydia trachomatis. J Infect Dis (1999) 0.83
Reading within the lines: naturally processed peptides displayed by MHC class I molecules. Curr Opin Immunol (1998) 0.82
Individuation of monoclonal anti-HPV16 E7 antibody linear peptide epitope by computational biology. Peptides (2001) 0.82
The calculus of immunity: quantitating antigen processing. Immunity (2003) 0.81
Impact of epitope permutations in the antibody response of mice to a multi-epitope polypeptide of the V3 loop of human immunodeficiency virus type 1. Biomol Eng (2001) 0.79
Pneumococcal and influenza vaccination: current situation and future prospects. Thorax (2002) 0.79
Insights from MHC-bound peptides. Novartis Found Symp (2003) 0.79
Timing of antiretroviral therapy: an immunological perspective. J HIV Ther (2003) 0.78
A conjugate vaccine for the prevention of pediatric pneumococcal disease. Mil Med (2002) 0.78
Generating data for databases--the peptide repertoire of HLA molecules. Novartis Found Symp (2003) 0.77
Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother (2012) 13.77
CD4+ T cells are required for secondary expansion and memory in CD8+ T lymphocytes. Nature (2003) 10.16
Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol (2012) 8.15
The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol (2005) 7.40
The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res (2004) 7.03
Adjuvant-enhanced antibody responses in the absence of toll-like receptor signaling. Science (2006) 6.47
Reversion of CTL escape-variant immunodeficiency viruses in vivo. Nat Med (2004) 6.33
The immune epitope database 2.0. Nucleic Acids Res (2009) 6.07
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci (2003) 5.94
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Cutting edge: the conversion of arginine to citrulline allows for a high-affinity peptide interaction with the rheumatoid arthritis-associated HLA-DRB1*0401 MHC class II molecule. J Immunol (2003) 4.64
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. Nucleic Acids Res (2008) 4.53
A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus. Nat Biotechnol (2006) 4.52
Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population. Proc Natl Acad Sci U S A (2009) 4.47
Improved method for predicting linear B-cell epitopes. Immunome Res (2006) 4.32
Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in human immunodeficiency virus type 1 infection. J Virol (2004) 4.20
NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS One (2007) 3.99
CD4+ T-cell help controls CD8+ T-cell memory via TRAIL-mediated activation-induced cell death. Nature (2005) 3.81
Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol (2014) 3.75
Dynamic programming of CD8+ T lymphocyte responses. Nat Immunol (2003) 3.73
A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol (2006) 3.73
Human circulating PD-1+CXCR3-CXCR5+ memory Tfh cells are highly functional and correlate with broadly neutralizing HIV antibody responses. Immunity (2013) 3.72
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics (2004) 3.72
A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol (2008) 3.71
Spindle checkpoint protein dynamics at kinetochores in living cells. Curr Biol (2004) 3.67
NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics (2008) 3.59
Rational HIV immunogen design to target specific germline B cell receptors. Science (2013) 3.55
Effectors and memories: Bcl-6 and Blimp-1 in T and B lymphocyte differentiation. Nat Immunol (2010) 3.48
HLA class I supertypes: a revised and updated classification. BMC Immunol (2008) 3.47
Identification of poxvirus CD8+ T cell determinants to enable rational design and characterization of smallpox vaccines. J Exp Med (2004) 3.43
Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci (2006) 3.06
Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics (2005) 2.99
The generation of protective memory-like CD8+ T cells during homeostatic proliferation requires CD4+ T cells. Nat Immunol (2006) 2.96
Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics (2005) 2.91
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics (2007) 2.83
Cellular immune selection with hepatitis C virus persistence in humans. J Exp Med (2005) 2.75
Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. Bioinformatics (2008) 2.69
Ab and T cell epitopes of influenza A virus, knowledge and opportunities. Proc Natl Acad Sci U S A (2007) 2.67
Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics (2010) 2.53
NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics (2009) 2.50
Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan. PLoS Comput Biol (2008) 2.48
Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes. Proc Natl Acad Sci U S A (2008) 2.43
A critical role for Stat3 signaling in immune tolerance. Immunity (2003) 2.41
The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics (2005) 2.40
Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data. Proc Natl Acad Sci U S A (2003) 2.38
A roadmap for the immunomics of category A-C pathogens. Immunity (2005) 2.36
Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells. Proc Natl Acad Sci U S A (2013) 2.32
ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics (2008) 2.26
Naive precursor frequencies and MHC binding rather than the degree of epitope diversity shape CD8+ T cell immunodominance. J Immunol (2008) 2.25
Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother (2012) 2.23
Comprehensive analysis of human immunodeficiency virus type 1-specific CD4 responses reveals marked immunodominance of gag and nef and the presence of broadly recognized peptides. J Virol (2004) 2.21
An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol (2005) 2.19
Relapse or eradication of cancer is predicted by peptide-major histocompatibility complex affinity. Cancer Cell (2013) 2.18
Asthma disease management: regression to the mean or better? Am J Manag Care (2004) 2.15
Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res (2008) 2.14