Published in Protein Sci on December 02, 2004
Improved method for predicting linear B-cell epitopes. Immunome Res (2006) 4.32
Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci (2006) 3.06
Predicting linear B-cell epitopes using string kernels. J Mol Recognit (2008) 2.47
AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res (2005) 2.40
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Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry. Mol Cell Proteomics (2011) 1.52
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Immunoinformatics comes of age. PLoS Comput Biol (2006) 1.35
Predicting flexible length linear B-cell epitopes. Comput Syst Bioinformatics Conf (2008) 1.32
Recent advances in B-cell epitope prediction methods. Immunome Res (2010) 1.26
Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models. BMC Bioinformatics (2006) 1.22
EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC Bioinformatics (2010) 1.21
Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature. BMC Bioinformatics (2011) 1.20
Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis. BMC Bioinformatics (2008) 1.15
The structural basis of antibody-antigen recognition. Front Immunol (2013) 1.14
Emerging vaccine informatics. J Biomed Biotechnol (2011) 1.12
SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction. BMC Genomics (2010) 1.12
Prediction of antigenic epitopes on protein surfaces by consensus scoring. BMC Bioinformatics (2009) 1.12
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
Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods. PLoS One (2013) 1.07
Vaccines: from empirical development to rational design. PLoS Pathog (2012) 1.01
Design and utilization of epitope-based databases and predictive tools. Immunogenetics (2010) 1.00
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Designing immunogenic peptides. Nat Chem Biol (2013) 0.99
An integrated approach to epitope analysis II: A system for proteomic-scale prediction of immunological characteristics. Immunome Res (2010) 0.98
Analysis and prediction of protective continuous B-cell epitopes on pathogen proteins. Immunome Res (2008) 0.98
High-throughput prediction of protein antigenicity using protein microarray data. Bioinformatics (2010) 0.97
PEPOP: computational design of immunogenic peptides. BMC Bioinformatics (2008) 0.96
Computer aided selection of candidate vaccine antigens. Immunome Res (2010) 0.95
Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames). BMC Struct Biol (2009) 0.95
Detecting patches of protein sites of influenza A viruses under positive selection. Mol Biol Evol (2012) 0.95
Mining for the antibody-antigen interacting associations that predict the B cell epitopes. BMC Struct Biol (2010) 0.95
Determinants of antigenicity and specificity in immune response for protein sequences. BMC Bioinformatics (2011) 0.94
Computational prediction of conformational B-cell epitopes from antigen primary structures by ensemble learning. PLoS One (2012) 0.93
Bioinformatics resources and tools for conformational B-cell epitope prediction. Comput Math Methods Med (2013) 0.92
Identification of a highly antigenic linear B cell epitope within Plasmodium vivax apical membrane antigen 1 (AMA-1). PLoS One (2011) 0.92
Impact of immunization technology and assay application on antibody performance--a systematic comparative evaluation. PLoS One (2011) 0.91
Prediction of B-cell epitopes using evolutionary information and propensity scales. BMC Bioinformatics (2013) 0.91
Computational vaccinology and the ICoVax 2012 workshop. BMC Bioinformatics (2013) 0.91
Peptide immunoaffinity enrichment coupled with mass spectrometry for peptide and protein quantification. Clin Lab Med (2011) 0.91
Evaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus. PLoS One (2013) 0.88
Peptide microarray analysis of in silico-predicted epitopes for serological diagnosis of Toxoplasma gondii infection in humans. Clin Vaccine Immunol (2012) 0.88
Structure of allergens and structure based epitope predictions. Methods (2013) 0.86
Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens. J Immunol Res (2015) 0.85
An analysis of B-cell epitope discontinuity. Mol Immunol (2012) 0.85
Diagnostic peptide discovery: prioritization of pathogen diagnostic markers using multiple features. PLoS One (2012) 0.85
Benchmarking B-cell epitope prediction for the design of peptide-based vaccines: problems and prospects. J Biomed Biotechnol (2010) 0.85
Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions. BMC Bioinformatics (2013) 0.85
Identification of B cell epitopes of alcohol dehydrogenase allergen of Curvularia lunata. PLoS One (2011) 0.85
Rapid identification of novel immunodominant proteins and characterization of a specific linear epitope of Campylobacter jejuni. PLoS One (2013) 0.84
The epitope space of the human proteome. Protein Sci (2008) 0.84
T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges. Immunome Res (2010) 0.84
B-Pred, a structure based B-cell epitopes prediction server. Adv Appl Bioinform Chem (2012) 0.82
Identification of amino acid propensities that are strong determinants of linear B-cell epitope using neural networks. PLoS One (2012) 0.81
Tertiary structure-based prediction of conformational B-cell epitopes through B factors. Bioinformatics (2014) 0.81
A computational assay to design an epitope-based Peptide vaccine against saint louis encephalitis virus. Bioinform Biol Insights (2013) 0.81
Applying bioinformatics for antibody epitope prediction using affinity-selected mimotopes - relevance for vaccine design. Immunome Res (2010) 0.81
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. Clin Dev Immunol (2013) 0.80
Structure and functional features of olive pollen pectin methylesterase using homology modeling and molecular docking methods. J Mol Model (2012) 0.80
Proposing low-similarity peptide vaccines against Mycobacterium tuberculosis. J Biomed Biotechnol (2010) 0.80
Immunoinformatics and epitope prediction in the age of genomic medicine. Genome Med (2015) 0.79
The self/nonself issue: A confrontation between proteomes. Self Nonself (2010) 0.79
Parallel immunizations of rabbits using the same antigen yield antibodies with similar, but not identical, epitopes. PLoS One (2012) 0.78
Antibody specific epitope prediction-emergence of a new paradigm. Curr Opin Virol (2015) 0.78
Serotyping of Toxoplasma gondii in cats (Felis domesticus) reveals predominance of type II infections in Germany. PLoS One (2013) 0.78
EPMLR: sequence-based linear B-cell epitope prediction method using multiple linear regression. BMC Bioinformatics (2014) 0.77
A minimal model of peptide binding predicts ensemble properties of serum antibodies. BMC Genomics (2012) 0.77
Peptide-based immunotherapeutics and vaccines. J Immunol Res (2014) 0.77
Prediction of peptide reactivity with human IVIg through a knowledge-based approach. PLoS One (2011) 0.77
Prediction of antibody response using recombinant human protein fragments as antigen. Protein Sci (2009) 0.77
Predicting linear B-cell epitopes using amino acid anchoring pair composition. BioData Min (2015) 0.76
Benchmarking B-cell epitope prediction with quantitative dose-response data on antipeptide antibodies: towards novel pharmaceutical product development. Biomed Res Int (2014) 0.76
Structure-Based Reverse Vaccinology Failed in the Case of HIV Because it Disregarded Accepted Immunological Theory. Int J Mol Sci (2016) 0.75
SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence. BMC Bioinformatics (2017) 0.75
Classification epitopes in groups based on their protein family. BMC Bioinformatics (2015) 0.75
In silico prediction of B cell epitopes of the extracellular domain of insulin-like growth factor-1 receptor. Mol Biol Res Commun (2016) 0.75
Inadequate Reference Datasets Biased toward Short Non-epitopes Confound B-cell Epitope Prediction. J Biol Chem (2016) 0.75
Proteomic peptide scan of porphyromonas gingivalis fima type ii for searching potential b-cell epitopes. Oral Implantol (Rome) (2016) 0.75
An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction. J Immunol Res (2016) 0.75
DRREP: deep ridge regressed epitope predictor. BMC Genomics (2017) 0.75
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JenPep: a novel computational information resource for immunobiology and vaccinology. J Chem Inf Comput Sci (2003) 1.64
A dominant linear B-cell epitope of ricin A-chain is the target of a neutralizing antibody response in Hodgkin's lymphoma patients treated with an anti-CD25 immunotoxin. Clin Exp Immunol (2004) 1.54
An assessment of prediction methods for locating continuous epitopes in proteins. Immunol Lett (1988) 1.24
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Identification of two antigenic epitopes on SARS-CoV spike protein. Biochem Biophys Res Commun (2004) 1.15
[Anti-cyclic citrullinated peptide antibodies as a diagnostic test for rheumatoid arthritis]. Harefuah (2003) 0.98
Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response. J Exp Med (2004) 3.48
VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics (2007) 2.10
JenPep: a database of quantitative functional peptide data for immunology. Bioinformatics (2002) 1.75
Identifiying human MHC supertypes using bioinformatic methods. J Immunol (2004) 1.72
JenPep: a novel computational information resource for immunobiology and vaccinology. J Chem Inf Comput Sci (2003) 1.64
Analysis of peptide-protein binding using amino acid descriptors: prediction and experimental verification for human histocompatibility complex HLA-A0201. J Med Chem (2005) 1.62
SVRMHC prediction server for MHC-binding peptides. BMC Bioinformatics (2006) 1.59
In silico identification of supertypes for class II MHCs. J Immunol (2005) 1.52
MHCPred: A server for quantitative prediction of peptide-MHC binding. Nucleic Acids Res (2003) 1.48
Benchmarking pK(a) prediction. BMC Biochem (2006) 1.47
Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores. BMC Bioinformatics (2006) 1.41
Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties. Vaccine (2006) 1.37
In silico identified CCR4 antagonists target regulatory T cells and exert adjuvant activity in vaccination. Proc Natl Acad Sci U S A (2008) 1.34
EpiJen: a server for multistep T cell epitope prediction. BMC Bioinformatics (2006) 1.26
Additive method for the prediction of protein-peptide binding affinity. Application to the MHC class I molecule HLA-A*0201. J Proteome Res (2003) 1.23
Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models. BMC Bioinformatics (2006) 1.22
Harnessing bioinformatics to discover new vaccines. Drug Discov Today (2007) 1.22
MHCPred: bringing a quantitative dimension to the online prediction of MHC binding. Appl Bioinformatics (2003) 1.19
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Towards the chemometric dissection of peptide--HLA-A*0201 binding affinity: comparison of local and global QSAR models. J Comput Aided Mol Des (2005) 1.11
PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values. Nucleic Acids Res (2006) 1.10
FIMM, a database of functional molecular immunology: update 2002. Nucleic Acids Res (2002) 1.06
Mycobacterium tuberculosis peptides presented by HLA-E molecules are targets for human CD8 T-cells with cytotoxic as well as regulatory activity. PLoS Pathog (2010) 1.06
Transporter associated with antigen processing preselection of peptides binding to the MHC: a bioinformatic evaluation. J Immunol (2004) 1.04
BPROMPT: A consensus server for membrane protein prediction. Nucleic Acids Res (2003) 1.03
On the hierarchical classification of G protein-coupled receptors. Bioinformatics (2007) 1.01
Toward an atomistic understanding of the immune synapse: large-scale molecular dynamics simulation of a membrane-embedded TCR-pMHC-CD4 complex. Mol Immunol (2007) 1.01
Quantitative online prediction of peptide binding to the major histocompatibility complex. J Mol Graph Model (2004) 1.01
LIPPRED: A web server for accurate prediction of lipoprotein signal sequences and cleavage sites. Bioinformation (2006) 1.01
Physicochemical explanation of peptide binding to HLA-A*0201 major histocompatibility complex: a three-dimensional quantitative structure-activity relationship study. Proteins (2002) 1.00
MHC class I bound to an immunodominant Theileria parva epitope demonstrates unconventional presentation to T cell receptors. PLoS Pathog (2010) 0.99
Greater CD8+ TCR heterogeneity and functional flexibility in HIV-2 compared to HIV-1 infection. J Immunol (2003) 0.99
HLA-A3 supermotif defined by quantitative structure-activity relationship analysis. Protein Eng (2003) 0.97
On the hydrophobicity of peptides: Comparing empirical predictions of peptide log P values. Bioinformation (2006) 0.97
Coupling in silico and in vitro analysis of peptide-MHC binding: a bioinformatic approach enabling prediction of superbinding peptides and anchorless epitopes. J Immunol (2004) 0.97
Molecular basis of peptide recognition by the TCR: affinity differences calculated using large scale computing. J Immunol (2005) 0.96
Proteomic applications of automated GPCR classification. Proteomics (2007) 0.95
Evolutionary dynamics of hepatitis C virus envelope genes during chronic infection. J Gen Virol (2005) 0.95
New horizons in mouse immunoinformatics: reliable in silico prediction of mouse class I histocompatibility major complex peptide binding affinity. Org Biomol Chem (2004) 0.92
Toward prediction of class II mouse major histocompatibility complex peptide binding affinity: in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique. J Chem Inf Model (2006) 0.91
Peptide binding prediction for the human class II MHC allele HLA-DP2: a molecular docking approach. BMC Struct Biol (2011) 0.91
A comparative molecular similarity index analysis (CoMSIA) study identifies an HLA-A2 binding supermotif. J Comput Aided Mol Des (2003) 0.90
Immunoinformatics. Predicting immunogenicity in silico. Preface. Methods Mol Biol (2007) 0.90
MHCPred 2.0: an updated quantitative T-cell epitope prediction server. Appl Bioinformatics (2006) 0.90
Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide: can the alpha3 and beta2m domains be neglected? J Comput Chem (2004) 0.88
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
Peptide length significantly influences in vitro affinity for MHC class II molecules. Immunome Res (2008) 0.88
Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations. Philos Trans A Math Phys Eng Sci (2005) 0.87
Toward the discovery of vaccine adjuvants: coupling in silico screening and in vitro analysis of antagonist binding to human and mouse CCR4 receptors. PLoS One (2009) 0.86
Peptide binding to the HLA-DRB1 supertype: a proteochemometrics analysis. Eur J Med Chem (2009) 0.86
Class I T-cell epitope prediction: improvements using a combination of proteasome cleavage, TAP affinity, and MHC binding. Mol Immunol (2006) 0.86
Toward bacterial protein sub-cellular location prediction: single-class discrimminant models for all gram- and gram+ compartments. Bioinformation (2006) 0.85
In silico prediction of peptide-MHC binding affinity using SVRMHC. Methods Mol Biol (2007) 0.85
Multi-class subcellular location prediction for bacterial proteins. Bioinformation (2006) 0.84
Toward the atomistic simulation of T cell epitopes automated construction of MHC: peptide structures for free energy calculations. J Mol Graph Model (2007) 0.84
Optimizing amino acid groupings for GPCR classification. Bioinformatics (2008) 0.84
Predicting class I major histocompatibility complex (MHC) binders using multivariate statistics: comparison of discriminant analysis and multiple linear regression. J Chem Inf Model (2007) 0.83
EpiTOP--a proteochemometric tool for MHC class II binding prediction. Bioinformatics (2010) 0.83
Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity. BMC Struct Biol (2006) 0.83
Integrating in silico and in vitro analysis of peptide binding affinity to HLA-Cw*0102: a bioinformatic approach to the prediction of new epitopes. PLoS One (2009) 0.83
Modeling the peptide-T cell receptor interaction by the comparative molecular similarity indices analysis-soft independent modeling of class analogy technique. J Med Chem (2006) 0.83
Immunoinformatic evaluation of multiple epitope ensembles as vaccine candidates: E coli 536. Bioinformation (2012) 0.82
GPCRTree: online hierarchical classification of GPCR function. BMC Res Notes (2008) 0.82
Quantitative approaches to computational vaccinology. Immunol Cell Biol (2002) 0.82
AllerTOP--a server for in silico prediction of allergens. BMC Bioinformatics (2013) 0.82
Identification of the HLA-DM/HLA-DR interface. Mol Immunol (2007) 0.81
An update on the functional molecular immunology (FIMM) database. Appl Bioinformatics (2005) 0.81
TATPred: a Bayesian method for the identification of twin arginine translocation pathway signal sequences. Bioinformation (2006) 0.81
Quantitative structure-activity relationships and the prediction of MHC supermotifs. Methods (2004) 0.80
Combining algorithms to predict bacterial protein sub-cellular location: Parallel versus concurrent implementations. Bioinformation (2006) 0.79
Lipocalins in bioscience: the first family gathering. Bioessays (2004) 0.79
Novel perforin mutation in a patient with hemophagocytic lymphohistiocytosis and CD45 abnormal splicing. Am J Med Genet A (2003) 0.79
A comparative molecular similarity indices (CoMSIA) study of peptide binding to the HLA-A3 superfamily. Bioorg Med Chem (2003) 0.79
Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity: in silico bioinformatic step-by-step guide using quantitative structure-activity relationships. Methods Mol Biol (2007) 0.79
Receptor-ligand binding sites and virtual screening. Curr Med Chem (2006) 0.79
From 'perfect mix' to 'potion magique'-- regulatory T cells and anti-inflammatory cytokines as adjuvant targets. Nat Rev Microbiol (2008) 0.79
MHC Class II Binding Prediction-A Little Help from a Friend. J Biomed Biotechnol (2010) 0.78
Using databases and data mining in vaccinology. Expert Opin Drug Discov (2007) 0.78
Beta barrel trans-membrane proteins: Enhanced prediction using a Bayesian approach. Bioinformation (2006) 0.78
Empirical prediction of peptide octanol-water partition coefficients. Bioinformation (2006) 0.78
Static energy analysis of MHC class I and class II peptide-binding affinity. Methods Mol Biol (2007) 0.77
Present perspectives on the automated classification of the G-protein coupled receptors (GPCRs) at the protein sequence level. Curr Top Med Chem (2011) 0.76
In silico identification of novel G protein coupled receptors. Methods Mol Biol (2009) 0.76
HLA-DP2 binding prediction by molecular dynamics simulations. Protein Sci (2011) 0.76
EpiDOCK: a molecular docking-based tool for MHC class II binding prediction. Protein Eng Des Sel (2013) 0.76
Histidine hydrogen bonding in MHC at pH 5 and pH 7 modeled by molecular docking and molecular dynamics simulations. Curr Comput Aided Drug Des (2014) 0.76
Molecular dynamics simulations: bring biomolecular structures alive on a computer. Methods Mol Biol (2007) 0.76
AllerTOP v.2--a server for in silico prediction of allergens. J Mol Model (2014) 0.76
DSD--an integrated, web-accessible database of Dehydrogenase Enzyme Stereospecificities. BMC Bioinformatics (2005) 0.75
A predictor of membrane class: Discriminating alpha-helical and beta-barrel membrane proteins from non-membranous proteins. Bioinformation (2006) 0.75
The classification of HLA supertypes by GRID/CPCA and hierarchical clustering methods. Methods Mol Biol (2007) 0.75
Discriminating antigen and non-antigen using proteome dissimilarity II: viral and fungal antigens. Bioinformation (2010) 0.75
Alpha helical trans-membrane proteins: Enhanced prediction using a Bayesian approach. Bioinformation (2006) 0.75
Discriminating antigen and non-antigen using proteome dissimilarity III: tumour and parasite antigens. Bioinformation (2010) 0.75
Discriminating antigen and non-antigen using proteome dissimilarity: bacterial antigens. Bioinformation (2010) 0.75
Peptide binding to HLA-DP proteins at pH 5.0 and pH 7.0: a quantitative molecular docking study. BMC Struct Biol (2012) 0.75