Published in PLoS Comput Biol on June 09, 2006
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
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
A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol (2008) 3.71
Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection. Nature (2010) 3.57
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics (2007) 2.83
Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics (2010) 2.53
Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan. PLoS Comput Biol (2008) 2.48
Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. BMC Immunol (2008) 2.30
Reverse vaccinology: developing vaccines in the era of genomics. Immunity (2010) 2.25
Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research. BMC Bioinformatics (2008) 2.17
Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res (2008) 2.14
Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries. Immunome Res (2008) 2.07
Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics (2007) 2.05
Nitrated alpha-synuclein immunity accelerates degeneration of nigral dopaminergic neurons. PLoS One (2008) 1.99
Immunodominant tuberculosis CD8 antigens preferentially restricted by HLA-B. PLoS Pathog (2007) 1.78
Evolutionarily conserved protein sequences of influenza a viruses, avian and human, as vaccine targets. PLoS One (2007) 1.72
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. J Immunol (2009) 1.57
NetMHCcons: a consensus method for the major histocompatibility complex class I predictions. Immunogenetics (2011) 1.57
Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development. J Biomed Biotechnol (2010) 1.55
Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods. Bioinformatics (2008) 1.53
Prediction of epitopes using neural network based methods. J Immunol Methods (2010) 1.35
HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity. J Immunol (2013) 1.32
The MHC class I peptide repertoire is molded by the transcriptome. J Exp Med (2008) 1.31
HLA class I binding of HBZ determines outcome in HTLV-1 infection. PLoS Pathog (2010) 1.28
Measurement of MHC/peptide interactions by gel filtration or monoclonal antibody capture. Curr Protoc Immunol (2013) 1.24
Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior. BMC Bioinformatics (2009) 1.23
Major histocompatibility complex class I binding predictions as a tool in epitope discovery. Immunology (2010) 1.21
NNAlign: a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data. PLoS One (2011) 1.20
Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput Biol (2013) 1.19
TEPITOPEpan: extending TEPITOPE for peptide binding prediction covering over 700 HLA-DR molecules. PLoS One (2012) 1.18
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
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
Amino acid similarity accounts for T cell cross-reactivity and for "holes" in the T cell repertoire. PLoS One (2008) 1.11
The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding. Bioinformatics (2009) 1.08
Applications for T-cell epitope queries and tools in the Immune Epitope Database and Analysis Resource. J Immunol Methods (2010) 1.07
Strength in numbers: achieving greater accuracy in MHC-I binding prediction by combining the results from multiple prediction tools. Immunome Res (2007) 1.06
A mathematical framework for the selection of an optimal set of peptides for epitope-based vaccines. PLoS Comput Biol (2008) 1.06
Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry. Mol Cell Proteomics (2015) 1.05
A critical cross-validation of high throughput structural binding prediction methods for pMHC. J Comput Aided Mol Des (2009) 1.03
Design and utilization of epitope-based databases and predictive tools. Immunogenetics (2010) 1.00
T-cell epitope prediction: rescaling can mask biological variation between MHC molecules. PLoS Comput Biol (2009) 0.99
From functional genomics to functional immunomics: new challenges, old problems, big rewards. PLoS Comput Biol (2006) 0.99
Designing immunogenic peptides. Nat Chem Biol (2013) 0.99
Prediction of supertype-specific HLA class I binding peptides using support vector machines. J Immunol Methods (2007) 0.98
Characterization of the peptide-binding specificity of the chimpanzee class I alleles A 0301 and A 0401 using a combinatorial peptide library. Immunogenetics (2007) 0.97
Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire. PLoS Comput Biol (2012) 0.97
Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. BMC Bioinformatics (2008) 0.96
State of the art and challenges in sequence based T-cell epitope prediction. Immunome Res (2010) 0.95
A probabilistic meta-predictor for the MHC class II binding peptides. Immunogenetics (2007) 0.95
Exploiting physico-chemical properties in string kernels. BMC Bioinformatics (2010) 0.93
Dana-Farber repository for machine learning in immunology. J Immunol Methods (2011) 0.93
The immune epitope database: a historical retrospective of the first decade. Immunology (2012) 0.93
Large-scale characterization of peptide-MHC binding landscapes with structural simulations. Proc Natl Acad Sci U S A (2011) 0.92
Limitations of Ab initio predictions of peptide binding to MHC class II molecules. PLoS One (2010) 0.92
Machine Learning Methods for Predicting HLA-Peptide Binding Activity. Bioinform Biol Insights (2015) 0.92
Automated benchmarking of peptide-MHC class I binding predictions. Bioinformatics (2015) 0.92
Peptide binding prediction for the human class II MHC allele HLA-DP2: a molecular docking approach. BMC Struct Biol (2011) 0.91
EpiToolKit--a web server for computational immunomics. Nucleic Acids Res (2008) 0.91
Bioinformatics for cancer immunology and immunotherapy. Cancer Immunol Immunother (2012) 0.90
HIV-1 vaccine-induced T-cell responses cluster in epitope hotspots that differ from those induced in natural infection with HIV-1. PLoS Pathog (2013) 0.90
Predicting MHC class I epitopes in large datasets. BMC Bioinformatics (2010) 0.90
Therapeutic Vaccine Strategies against Human Papillomavirus. Vaccines (Basel) (2014) 0.89
A novel strategy for classifying the output from an in silico vaccine discovery pipeline for eukaryotic pathogens using machine learning algorithms. BMC Bioinformatics (2013) 0.89
Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy? Expert Rev Vaccines (2012) 0.88
Prediction of MHC binding peptide using Gibbs motif sampler, weight matrix and artificial neural network. Bioinformation (2008) 0.87
The distribution of CTL epitopes in HIV-1 appears to be random, and similar to that of other proteomes. BMC Evol Biol (2009) 0.86
MetaMHC: a meta approach to predict peptides binding to MHC molecules. Nucleic Acids Res (2010) 0.86
Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions. BMC Bioinformatics (2014) 0.85
Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands. PLoS One (2009) 0.85
The role of MHC class I allele Mamu-A*07 during SIV(mac)239 infection. Immunogenetics (2011) 0.85
Identification of naturally processed ligands in the C57BL/6 mouse using large-scale mass spectrometric peptide sequencing and bioinformatics prediction. Immunogenetics (2009) 0.85
The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP. PLoS One (2008) 0.85
T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges. Immunome Res (2010) 0.84
PeptX: using genetic algorithms to optimize peptides for MHC binding. BMC Bioinformatics (2011) 0.83
The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference. J Immunol (2016) 0.82
Positional bias of MHC class I restricted T-cell epitopes in viral antigens is likely due to a bias in conservation. PLoS Comput Biol (2013) 0.82
Unexpected diversity of cellular immune responses against Nef and Vif in HIV-1-infected patients who spontaneously control viral replication. PLoS One (2010) 0.82
Predicting HLA class I non-permissive amino acid residues substitutions. PLoS One (2012) 0.82
EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information. BMC Bioinformatics (2012) 0.81
The Human Proteome Organization Chromosome 6 Consortium: integrating chromosome-centric and biology/disease driven strategies. J Proteomics (2013) 0.80
Scrutinizing MHC-I binding peptides and their limits of variation. PLoS Comput Biol (2013) 0.80
Immunoinformatics and epitope prediction in the age of genomic medicine. Genome Med (2015) 0.79
Prediction of peptides binding to MHC class I and II alleles by temporal motif mining. BMC Bioinformatics (2013) 0.79
The efficiency of the human CD8+ T cell response: how should we quantify it, what determines it, and does it matter? PLoS Comput Biol (2012) 0.79
An efficient T-cell epitope discovery strategy using in silico prediction and the iTopia assay platform. Oncoimmunology (2012) 0.78
T-cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome. Immunology (2016) 0.78
Zooming into the binding groove of HLA molecules: which positions and which substitutions change peptide binding most? Immunogenetics (2015) 0.78
MHC Class II Binding Prediction-A Little Help from a Friend. J Biomed Biotechnol (2010) 0.78
The common equine class I molecule Eqca-1*00101 (ELA-A3.1) is characterized by narrow peptide binding and T cell epitope repertoires. Immunogenetics (2015) 0.78
The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design. Front Immunol (2017) 0.77
Peptide-based immunotherapeutics and vaccines. J Immunol Res (2014) 0.77
Comparison of experimental fine-mapping to in silico prediction results of HIV-1 epitopes reveals ongoing need for mapping experiments. Immunology (2014) 0.77
No longer confidential: estimating the confidence of individual regression predictions. PLoS One (2012) 0.77
Residue analysis of a CTL epitope of SARS-CoV spike protein by IFN-gamma production and bioinformatics prediction. BMC Immunol (2012) 0.77
Side-chain conformational space analysis (SCSA): a multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities. J Comput Aided Mol Des (2008) 0.77
Equivalent T cell epitope promiscuity in ecologically diverse human pathogens. PLoS One (2013) 0.76
HLA-DP2 binding prediction by molecular dynamics simulations. Protein Sci (2011) 0.76
Improving peptide-MHC class I binding prediction for unbalanced datasets. BMC Bioinformatics (2008) 0.76
Enhancing in silico protein-based vaccine discovery for eukaryotic pathogens using predicted peptide-MHC binding and peptide conservation scores. PLoS One (2014) 0.76
Identification of the peptide-binding motif recognized by the pigtail macaque class I MHC molecule Mane-A1*082:01 (Mane A*0301). Immunogenetics (2012) 0.76
Measuring the accuracy of diagnostic systems. Science (1988) 27.46
SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics (1999) 14.15
Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J Immunol (1994) 8.16
The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol (2005) 7.40
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci (2003) 5.94
The relationship between class I binding affinity and immunogenicity of potential cytotoxic T cell epitopes. J Immunol (1994) 4.37
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics (2004) 3.72
The design and implementation of the immune epitope database and analysis resource. Immunogenetics (2005) 3.00
Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics (2005) 2.99
Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens (2003) 2.93
Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics (2005) 2.91
Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics (2002) 2.66
Two complementary methods for predicting peptides binding major histocompatibility complex molecules. J Mol Biol (1997) 2.57
Producing nature's gene-chips: the generation of peptides for display by MHC class I molecules. Annu Rev Immunol (2001) 2.51
Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles. Immunogenetics (2004) 2.49
The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics (2005) 2.40
AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res (2005) 2.40
An essential role for tripeptidyl peptidase in the generation of an MHC class I epitope. Nat Immunol (2003) 2.38
MHCBN: a comprehensive database of MHC binding and non-binding peptides. Bioinformatics (2003) 2.36
Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding. Cell Mol Life Sci (2005) 2.32
Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol (2003) 2.31
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
Important role of cathepsin S in generating peptides for TAP-independent MHC class I crosspresentation in vivo. Immunity (2004) 2.13
ProPred1: prediction of promiscuous MHC Class-I binding sites. Bioinformatics (2003) 2.10
MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides. Nucleic Acids Res (2005) 2.05
Prediction of proteasome cleavage motifs by neural networks. Protein Eng (2002) 1.81
Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. Bioinformatics (2003) 1.71
Establishment of a quantitative ELISA capable of determining peptide - MHC class I interaction. Tissue Antigens (2002) 1.68
Tumors as elusive targets of T-cell-based active immunotherapy. Trends Immunol (2003) 1.67
Methods for prediction of peptide binding to MHC molecules: a comparative study. Mol Med (2002) 1.61
Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles. Protein Sci (2000) 1.58
SVM based method for predicting HLA-DRB1*0401 binding peptides in an antigen sequence. Bioinformatics (2004) 1.57
Analysis and prediction of affinity of TAP binding peptides using cascade SVM. Protein Sci (2004) 1.55
PAProC: a prediction algorithm for proteasomal cleavages available on the WWW. Immunogenetics (2001) 1.44
An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries. Immunogenetics (2000) 1.42
Population of the HLA ligand database. Tissue Antigens (2003) 1.38
Ligand dissociation constants from competition binding assays: errors associated with ligand depletion. Mol Pharmacol (1987) 1.36
MAPPP: MHC class I antigenic peptide processing prediction. Appl Bioinformatics (2003) 1.31
PREDBALB/c: a system for the prediction of peptide binding to H2d molecules, a haplotype of the BALB/c mouse. Nucleic Acids Res (2005) 1.20
MHCPred: bringing a quantitative dimension to the online prediction of MHC binding. Appl Bioinformatics (2003) 1.19
Classification of A1- and A24-supertype molecules by analysis of their MHC-peptide binding repertoires. Immunogenetics (2005) 1.18
PepDist: a new framework for protein-peptide binding prediction based on learning peptide distance functions. BMC Bioinformatics (2006) 1.10
A computational resource for the prediction of peptide binding to Indian rhesus macaque MHC class I molecules. Vaccine (2005) 1.08
TAP-independent antigen presentation on MHC class I molecules: lessons from Epstein-Barr virus. Microbes Infect (2003) 1.02
Simultaneous prediction of binding capacity for multiple molecules of the HLA B44 supertype. J Immunol (2003) 0.99
A neural network model approach to the study of human TAP transporter. In Silico Biol (1999) 0.95
Remnant epitopes generate autoimmunity: from rheumatoid arthritis and multiple sclerosis to diabetes. Adv Exp Med Biol (2003) 0.89
In silico prediction of peptide binding affinity to class I mouse major histocompatibility complexes: a comparative molecular similarity index analysis (CoMSIA) study. J Chem Inf Model (2005) 0.88
Proteasomes get by with lots of help from their friends. Immunity (2004) 0.84
The many faces of binding artefacts. Trends Pharmacol Sci (2000) 0.81
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26
Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother (2012) 13.77
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
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
A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Res (2010) 3.81
Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol (2014) 3.75
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
NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics (2008) 3.59
A generic method for assignment of reliability scores applied to solvent accessibility predictions. BMC Struct Biol (2009) 3.56
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
The design and implementation of the immune epitope database and analysis resource. Immunogenetics (2005) 3.00
Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics (2005) 2.99
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
The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics (2005) 2.40
Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics (2004) 2.39
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
Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Cell Metab (2013) 2.17
Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res (2008) 2.14