Are bacterial vaccine antigens T-cell epitope depleted?

[1]  V. Brusic,et al.  Evaluation of MHC class I peptide binding prediction servers: Applications for vaccine research , 2008, BMC Immunology.

[2]  O. Pybus,et al.  Analysis of the Evolutionary Forces in an Immunodominant CD8 Epitope in Hepatitis C Virus at a Population Level , 2008, Journal of Virology.

[3]  Morten Nielsen,et al.  Modeling the adaptive immune system: predictions and simulations , 2007, Bioinform..

[4]  Vladimir Brusic,et al.  Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms , 2007, BMC Bioinformatics.

[5]  R. Medzhitov.  Recognition of microorganisms and activation of the immune response , 2007, Nature.

[6]  Morten Nielsen,et al.  Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method , 2007, BMC Bioinformatics.

[7]  Matthew N Davies,et al.  Harnessing bioinformatics to discover new vaccines. , 2007, Drug discovery today.

[8]  Gajendra P.S. Raghava,et al.  A hybrid approach for predicting promiscuous MHC class I restricted T cell epitopes , 2007, Journal of Biosciences.

[9]  E. Appella,et al.  The Wild-Type Sequence (wt) p5325–35 Peptide Induces HLA-DR7 and HLA-DR11-Restricted CD4+ Th Cells Capable of Enhancing the Ex Vivo Expansion and Function of Anti-wt p53264–272 Peptide CD8+ T Cells1 , 2006, The Journal of Immunology.

[10]  Tin Wee Tan,et al.  Methods and protocols for prediction of immunogenic epitopes , 2006, Briefings Bioinform..

[11]  Kuo-Chen Chou,et al.  Large-scale predictions of gram-negative bacterial protein subcellular locations. , 2006, Journal of proteome research.

[12]  V. Wiwanitkit.  Finding a T-cell epitope for a melanoma vaccine by an immunomics technique. , 2006, Asian Pacific journal of cancer prevention : APJCP.

[13]  A. Kang,et al.  Crystallographic Structure of a Rheumatoid Arthritis MHC Susceptibility Allele, HLA-DR1 (DRB1*0101), Complexed with the Immunodominant Determinant of Human Type II Collagen1 , 2006, The Journal of Immunology.

[14]  Morten Nielsen,et al.  A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules , 2006, PLoS Comput. Biol..

[15]  M. Cooper,et al.  The evolution of adaptive immunity. , 2006, Annual review of immunology.

[16]  Channa K. Hattotuwagama,et al.  Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity , 2006, BMC Structural Biology.

[17]  B. Finlay,et al.  Anti-Immunology: Evasion of the Host Immune System by Bacterial and Viral Pathogens , 2006, Cell.

[18]  D. Chaplin,et al.  1. Overview of the human immune response. , 2006, The Journal of allergy and clinical immunology.

[19]  O. Lund,et al.  An integrative approach to CTL epitope prediction: A combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions , 2005, European journal of immunology.

[20]  O. Lund,et al.  The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage , 2005, Immunogenetics.

[21]  Gajendra P.S. Raghava,et al.  Prediction of CTL epitopes using QM, SVM and ANN techniques. , 2004, Vaccine.

[22]  Alessandro Sette,et al.  Selection, Transmission, and Reversion of an Antigen-Processing Cytotoxic T-Lymphocyte Escape Mutation in Human Immunodeficiency Virus Type 1 Infection , 2004, Journal of Virology.

[23]  A. Meinke,et al.  Bacterial genomes pave the way to novel vaccines. , 2004, Current opinion in microbiology.

[24]  Amos Bairoch,et al.  Swiss-Prot: Juggling between evolution and stability , 2004, Briefings Bioinform..

[25]  Rob J. De Boer,et al.  MHC polymorphism under host-pathogen coevolution , 2004, Immunogenetics.

[26]  S Brunak,et al.  Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. , 2003, Tissue antigens.

[27]  Bryan Lingard,et al.  Analysis of Known Bacterial Protein Vaccine Antigens Reveals Biased Physical Properties and Amino Acid Composition , 2003, Comparative and functional genomics.

[28]  Bjoern Peters,et al.  Identifying MHC Class I Epitopes by Predicting the TAP Transport Efficiency of Epitope Precursors , 2003, The Journal of Immunology.

[29]  Manoj Bhasin,et al.  Prediction of promiscuous and high-affinity mutated MHC binders. , 2003, Hybridoma and hybridomics.

[30]  Gajendra P. S. Raghava,et al.  ProPred1: Prediction of Promiscuous MHC Class-I Binding Sites , 2003, Bioinform..

[31]  O. Lund,et al.  novel sequence representations Reliable prediction of T-cell epitopes using neural networks with , 2003 .

[32]  R. Rappuoli,et al.  Reverse vaccinology: a genome-based approach for vaccine development , 2002, Expert opinion on biological therapy.

[33]  Forest M White,et al.  Analysis of MHC Class II Antigen Processing by Quantitation of Peptides that Constitute Nested Sets , 2002, The Journal of Immunology.

[34]  Arne Elofsson,et al.  Prediction of MHC class I binding peptides, using SVMHC , 2002, BMC Bioinformatics.

[35]  E. Reinherz,et al.  Prediction of MHC class I binding peptides using profile motifs. , 2002, Human immunology.

[36]  Fabio Grassi,et al.  Identification of a Promiscuous T-Cell Epitope in Mycobacterium tuberculosis Mce Proteins , 2002, Infection and Immunity.

[37]  Gajendra P. S. Raghava,et al.  ProPred: prediction of HLA-DR binding sites , 2001, Bioinform..

[38]  G. Jung,et al.  From combinatorial libraries to MHC ligand motifs, T-cell superagonists and antagonists. , 2001, Biologicals : journal of the International Association of Biological Standardization.

[39]  Martin T. Swain,et al.  An automated approach to modelling class II MHC alleles and predicting peptide binding , 2001, Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001).

[40]  W. Maksymowych,et al.  Bacterial modulation of antigen processing and presentation. , 2000, Microbes and infection.

[41]  Peter Parham,et al.  The HLA FactsBook , 1999 .

[42]  H. Rammensee,et al.  SYFPEITHI: database for MHC ligands and peptide motifs , 1999, Immunogenetics.

[43]  U. Şahin,et al.  Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices , 1999, Nature Biotechnology.

[44]  P. Kareiva.  Coevolutionary arms races: is victory possible? , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[45]  D. Wiley,et al.  Toxic shock syndrome toxin-1 complexed with a class II major histocompatibility molecule HLA-DR1. , 1994, Science.

[46]  K Nishikawa,et al.  Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies. , 1994, Journal of molecular biology.

[47]  Don C. Wiley,et al.  Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide , 1994, Nature.

[48]  K. Parker,et al.  Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. , 1994, Journal of immunology.

[49]  T. Mosmann,et al.  IL-10 inhibits cytokine production by activated macrophages. , 1991, Journal of immunology.

[50]  Uthaman Gowthaman,et al.  In silico tools for predicting peptides binding to HLA-class II molecules: more confusion than conclusion. , 2008, Journal of proteome research.

[51]  David D. Chaplin,et al.  Overview of the human immune response , 2006 .

[52]  Channa K. Hattotuwagama,et al.  MHCPred 2.0: an updated quantitative T-cell epitope prediction server. , 2006, Applied bioinformatics.

[53]  Anne S De Groot,et al.  Immunomics: discovering new targets for vaccines and therapeutics. , 2006, Drug discovery today.

[54]  Channa K. Hattotuwagama,et al.  MHCPred 2.0 , 2006 .

[55]  Nicole Frahma,et al.  HIV Molecular Immunology 2005 , 2006 .

[56]  F. Sinigaglia,et al.  HLA class II peptide binding specificity and autoimmunity. , 1997, Advances in immunology.

[57]  S Kishimoto,et al.  [Trends in immunology]. , 1983, Nihon rinsho. Japanese journal of clinical medicine.