Published in J Chem Inf Model on January 22, 2007
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
In silico analysis of six known Leishmania major antigens and in vitro evaluation of specific epitopes eliciting HLA-A2 restricted CD8 T cell response. PLoS Negl Trop Dis (2011) 1.05
Computational prediction of broadly neutralizing HIV-1 antibody epitopes from neutralization activity data. PLoS One (2013) 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
A comprehensive analysis of the thermodynamic events involved in ligand-receptor binding using CoRIA and its variants. J Comput Aided Mol Des (2008) 0.78
Steric recognition of T-cell receptor contact residues is required to map mutant epitopes by immunoinformatical programmes. Immunology (2012) 0.75
Identification of HLA‑A*1101‑restricted cytotoxic T lymphocyte epitopes derived from epidermal growth factor pathway substrate number 8. Mol Med Rep (2016) 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
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
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
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
FIMM, a database of functional molecular immunology: update 2002. Nucleic Acids Res (2002) 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
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
Evolutionary dynamics of hepatitis C virus envelope genes during chronic infection. J Gen Virol (2005) 0.95
Proteomic applications of automated GPCR classification. Proteomics (2007) 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
Peptide binding prediction for the human class II MHC allele HLA-DP2: a molecular docking approach. BMC Struct Biol (2011) 0.91
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
A comparative molecular similarity index analysis (CoMSIA) study identifies an HLA-A2 binding supermotif. J Comput Aided Mol Des (2003) 0.90
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
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
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
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
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
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
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
Immunoinformatic evaluation of multiple epitope ensembles as vaccine candidates: E coli 536. Bioinformation (2012) 0.82
Quantitative approaches to computational vaccinology. Immunol Cell Biol (2002) 0.82
GPCRTree: online hierarchical classification of GPCR function. BMC Res Notes (2008) 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
TATPred: a Bayesian method for the identification of twin arginine translocation pathway signal sequences. Bioinformation (2006) 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
Lipocalins in bioscience: the first family gathering. Bioessays (2004) 0.79
From 'perfect mix' to 'potion magique'-- regulatory T cells and anti-inflammatory cytokines as adjuvant targets. Nat Rev Microbiol (2008) 0.79
Receptor-ligand binding sites and virtual screening. Curr Med Chem (2006) 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
A comparative molecular similarity indices (CoMSIA) study of peptide binding to the HLA-A3 superfamily. Bioorg Med Chem (2003) 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
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
Molecular dynamics simulations: bring biomolecular structures alive on a computer. Methods Mol Biol (2007) 0.76
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
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
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
DSD--an integrated, web-accessible database of Dehydrogenase Enzyme Stereospecificities. BMC Bioinformatics (2005) 0.75
Alpha helical trans-membrane proteins: Enhanced prediction using a Bayesian approach. 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
Discriminating antigen and non-antigen using proteome dissimilarity III: tumour and parasite 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
A predictor of membrane class: Discriminating alpha-helical and beta-barrel membrane proteins from non-membranous proteins. Bioinformation (2006) 0.75