Published in Vaccine on September 28, 2006
AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic Acids Res (2009) 1.18
High-throughput prediction of protein antigenicity using protein microarray data. Bioinformatics (2010) 0.97
Computer aided selection of candidate vaccine antigens. Immunome Res (2010) 0.95
Mature Epitope Density--a strategy for target selection based on immunoinformatics and exported prokaryotic proteins. BMC Genomics (2013) 0.82
Immunoproteomic identification of immunodominant antigens independent of the time of infection in Brucella abortus 2308-challenged cattle. Vet Res (2015) 0.82
A statistical physics perspective on alignment-independent protein sequence comparison. Bioinformatics (2015) 0.81
Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates. Proteomes (2016) 0.77
Genetic diversity of the Pneumococcal CbpA: Implications for next-generation vaccine development. Hum Vaccin Immunother (2015) 0.75
Discriminating antigen and non-antigen using proteome dissimilarity II: viral and fungal antigens. Bioinformation (2010) 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
Designing Epitope Ensemble Vaccines against TB by Selection: Prioritizing Antigens using Predicted Immunogenicity. Bioinformation (2017) 0.75
Alignment-free sequence comparison: benefits, applications, and tools. Genome Biol (2017) 0.75
Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response. J Exp Med (2004) 3.48
Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci (2004) 2.70
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
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
Bacterial bioinformatics: pathogenesis and the genome. J Mol Microbiol Biotechnol (2002) 1.18
AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic Acids Res (2009) 1.18
Computer-aided biotechnology: from immuno-informatics to reverse vaccinology. Trends Biotechnol (2008) 1.13
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
Quantitative online prediction of peptide binding to the major histocompatibility complex. J Mol Graph Model (2004) 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
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
On the hydrophobicity of peptides: Comparing empirical predictions of peptide log P values. Bioinformation (2006) 0.97
HLA-A3 supermotif defined by quantitative structure-activity relationship analysis. Protein Eng (2003) 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
MHCPred 2.0: an updated quantitative T-cell epitope prediction server. Appl Bioinformatics (2006) 0.90
Immunoinformatics. Predicting immunogenicity in silico. Preface. Methods Mol Biol (2007) 0.90
A comparative molecular similarity index analysis (CoMSIA) study identifies an HLA-A2 binding supermotif. J Comput Aided Mol Des (2003) 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
Class I T-cell epitope prediction: improvements using a combination of proteasome cleavage, TAP affinity, and MHC binding. Mol Immunol (2006) 0.86
Peptide binding to the HLA-DRB1 supertype: a proteochemometrics analysis. Eur J Med Chem (2009) 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
Optimizing amino acid groupings for GPCR classification. Bioinformatics (2008) 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
Multi-class subcellular location prediction for bacterial proteins. Bioinformation (2006) 0.84
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
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
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
TATPred: a Bayesian method for the identification of twin arginine translocation pathway signal sequences. Bioinformation (2006) 0.81
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
Quantitative structure-activity relationships and the prediction of MHC supermotifs. Methods (2004) 0.80
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
Lipocalins in bioscience: the first family gathering. Bioessays (2004) 0.79
Receptor-ligand binding sites and virtual screening. Curr Med Chem (2006) 0.79
Combining algorithms to predict bacterial protein sub-cellular location: Parallel versus concurrent implementations. Bioinformation (2006) 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
From 'perfect mix' to 'potion magique'-- regulatory T cells and anti-inflammatory cytokines as adjuvant targets. Nat Rev Microbiol (2008) 0.79
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
MHC Class II Binding Prediction-A Little Help from a Friend. J Biomed Biotechnol (2010) 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
AllerTOP v.2--a server for in silico prediction of allergens. J Mol Model (2014) 0.76
HLA-DP2 binding prediction by molecular dynamics simulations. Protein Sci (2011) 0.76
In silico identification of novel G protein coupled receptors. Methods Mol Biol (2009) 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
Discriminating antigen and non-antigen using proteome dissimilarity III: tumour and parasite antigens. Bioinformation (2010) 0.75
Alpha helical trans-membrane proteins: Enhanced prediction using a Bayesian approach. Bioinformation (2006) 0.75
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: 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
Discriminating antigen and non-antigen using proteome dissimilarity II: viral and fungal antigens. Bioinformation (2010) 0.75