Stepwise identification of HLA-A*0201-restricted CD8+ T-cell epitope peptides from herpes simplex virus type 1 genome boosted by a StepRank scheme.
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Huilan Yang | Bingling Li | Zhongrong Liu | Jianyong Fan | Bingling Li | Jianjun Bi | Huilan Yang | Rengang Song | Jianjun Bi | Rengang Song | Chaoqin Long | Zhongrong Liu | Chao-qin Long | J. Fan | Jian-yong Fan
[1] David Heckerman,et al. Broad and Gag-Biased HIV-1 Epitope Repertoires Are Associated with Lower Viral Loads , 2008, PloS one.
[2] Alessandro Sette,et al. The Immune Epitope Database 2.0 , 2009, Nucleic Acids Res..
[3] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[4] Ken Chen,et al. Prediction of binding affinities between the human amphiphysin-1 SH3 domain and its peptide ligands using homology modeling, molecular dynamics and molecular field analysis. , 2005, Journal of proteome research.
[5] D. Flower,et al. Physicochemical explanation of peptide binding to HLA‐A*0201 major histocompatibility complex: A three‐dimensional quantitative structure‐activity relationship study , 2002, Proteins.
[6] Y. Hiasa,et al. Identification of CTL epitopes in hepatitis C virus by a genome-wide computational scanning and a rational design of peptide vaccine , 2007, Immunogenetics.
[7] Ellis L Reinherz,et al. Genome-wide Characterization of a Viral Cytotoxic T Lymphocyte Epitope Repertoire* , 2003, Journal of Biological Chemistry.
[8] Hanah Margalit,et al. A structure-based approach for prediction of MHC-binding peptides. , 2004, Methods.
[9] Irini Doytchinova,et al. The HLA-A2-supermotif: a QSAR definition. , 2003, Organic & biomolecular chemistry.
[10] S. Wold,et al. New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids. , 1998, Journal of medicinal chemistry.
[11] D. Flower,et al. Additive method for the prediction of protein-peptide binding affinity. Application to the MHC class I molecule HLA-A*0201. , 2002, Journal of proteome research.
[12] Yoshihiro Yamaguchi,et al. Roles for the Two-hybrid System in Exploration of the Yeast Protein Interactome* , 2002, Molecular & Cellular Proteomics.
[13] Naoki Abe,et al. Empirical Evaluation of a Dynamic Experiment Design Method for Prediction of MHC Class I-Binding Peptides1 , 2002, The Journal of Immunology.
[14] Pingping Guan,et al. Quantitative structure-activity relationships and the prediction of MHC supermotifs. , 2004, Methods.
[15] A. Tropsha,et al. Beware of q2! , 2002, Journal of molecular graphics & modelling.
[16] H. M. Geysen,et al. Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid. , 1984, Proceedings of the National Academy of Sciences of the United States of America.
[17] G. Welling,et al. B and T cell epitopes of glycoprotein D of herpes simplex virus type 1. , 1991, FEMS microbiology immunology.
[18] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[19] J. Leunissen,et al. Definition of natural T cell antigens with mimicry epitopes obtained from dedicated synthetic peptide libraries. , 1998, Journal of immunology.
[20] L. Payne,et al. Potent protective cellular immune responses generated by a DNA vaccine encoding HSV-2 ICP27 and the E. coli heat labile enterotoxin. , 2006, Vaccine.
[21] S. Wechsler,et al. The role of a glycoprotein K (gK) CD8+ T-cell epitope of herpes simplex virus on virus replication and pathogenicity. , 2009, Investigative ophthalmology & visual science.
[22] P. Visscher,et al. The Genetic Interpretation of Area under the ROC Curve in Genomic Profiling , 2010, PLoS genetics.
[23] A. Nesburn,et al. A Novel HLA (HLA-A*0201) Transgenic Rabbit Model for Preclinical Evaluation of Human CD8+ T Cell Epitope-Based Vaccines against Ocular Herpes , 2010, The Journal of Immunology.
[24] F. Aoki,et al. Glycoprotein-D-adjuvant vaccine to prevent genital herpes. , 2002, The New England journal of medicine.
[25] L. BenMohamed,et al. Gender-Dependent HLA-DR-Restricted Epitopes Identified from Herpes Simplex Virus Type 1 Glycoprotein D , 2008, Clinical and Vaccine Immunology.
[26] P. Kollman,et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. , 2000, Accounts of chemical research.
[27] Andrew J Davison,et al. Topics in herpesvirus genomics and evolution. , 2006, Virus research.
[28] Roland L. Dunbrack,et al. proteins STRUCTURE O FUNCTION O BIOINFORMATICS Improved prediction of protein side-chain conformations with SCWRL4 , 2022 .
[29] H. Rammensee,et al. Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules , 1991, Nature.
[30] H. Rammensee,et al. SYFPEITHI: database for MHC ligands and peptide motifs , 1999, Immunogenetics.
[31] M R Lee,et al. Use of MM‐PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece , 2000, Proteins.
[32] J. Sidney,et al. Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules , 1993, Cell.
[33] A. Nesburn,et al. Local Periocular Vaccination Protects against Eye Disease More Effectively Than Systemic Vaccination following Primary Ocular Herpes Simplex Virus Infection in Rabbits , 1998, Journal of Virology.
[34] A. Nesburn,et al. A therapeutic vaccine that reduces recurrent herpes simplex virus type 1 corneal disease. , 1998, Investigative ophthalmology & visual science.
[35] Vladimir Brusic,et al. Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms , 2007, BMC Bioinformatics.
[36] J. Scott,et al. Searching for peptide ligands with an epitope library. , 1990, Science.
[37] Irini A. Doytchinova,et al. Predicting Class I Major Histocompatibility Complex (MHC) Binders Using Multivariate Statistics: Comparison of Discriminant Analysis and Multiple Linear Regression , 2007, J. Chem. Inf. Model..
[38] A Sette,et al. Definition of specific peptide motifs for four major HLA-A alleles. , 1994, Journal of immunology.
[39] Hu Mei,et al. A set of new amino acid descriptors applied in prediction of MHC class I binding peptides. , 2009, European journal of medicinal chemistry.
[40] D. Flower,et al. Toward the quantitative prediction of T-cell epitopes: coMFA and coMSIA studies of peptides with affinity for the class I MHC molecule HLA-A*0201. , 2001, Journal of medicinal chemistry.
[41] F. Aoki,et al. Safety and immunogenicity of glycoprotein D-adjuvant genital herpes vaccine. , 2004, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[42] F. Tian,et al. In silico quantitative prediction of peptides binding affinity to human MHC molecule: an intuitive quantitative structure–activity relationship approach , 2009, Amino Acids.
[43] J. Schneider-Mergener,et al. Applications of peptide arrays prepared by the SPOT-technology. , 2001, Current opinion in biotechnology.
[44] S. Wold,et al. PLS-regression: a basic tool of chemometrics , 2001 .
[45] Ken Chen,et al. Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain , 2006, PLoS Comput. Biol..
[46] K. Lam,et al. Combinatorial peptide library methods for immunobiology research. , 2003, Experimental hematology.
[47] 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.
[48] R. Frank. The SPOT-synthesis technique. Synthetic peptide arrays on membrane supports--principles and applications. , 2002, Journal of immunological methods.
[49] W. Kwok,et al. Recognition of Herpes Simplex Virus Type 2 Tegument Proteins by CD4 T Cells Infiltrating Human Genital Herpes Lesions , 1998, Journal of Virology.
[50] K. Rosenthal,et al. Ligand epitope antigen presentation system vaccines against herpes simplex virus. , 2005, Frontiers in bioscience : a journal and virtual library.
[51] F. Tian,et al. A Structure‐based, Quantitative Structure–Activity Relationship Approach for Predicting HLA‐A*0201‐restricted Cytotoxic T Lymphocyte Epitopes , 2007, Chemical biology & drug design.
[52] Morten Nielsen,et al. A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules , 2006, PLoS Comput. Biol..
[53] J. Rajčáni,et al. Peculiarities of Herpes Simplex Virus (HSV) Transcription: An overview , 2004, Virus Genes.
[54] E. Reinherz,et al. Prediction of MHC class I binding peptides using profile motifs. , 2002, Human immunology.
[55] B. Roux,et al. Implicit solvent models. , 1999, Biophysical chemistry.
[56] Irini A. Doytchinova,et al. Towards the chemometric dissection of peptide – HLA-A*0201 binding affinity: comparison of local and global QSAR models , 2005, J. Comput. Aided Mol. Des..
[57] C. Pinilla,et al. Use of combinatorial peptide libraries for T-cell epitope mapping. , 2003, Methods.
[58] Andrew P. Bradley,et al. The use of the area under the ROC curve in the evaluation of machine learning algorithms , 1997, Pattern Recognit..
[59] Maria Jesus Martin,et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..
[60] W. Dunn,et al. Amino acid side chain descriptors for quantitative structure-activity relationship studies of peptide analogues. , 1995, Journal of medicinal chemistry.
[61] K. Lamberth,et al. HLA-A*0201-Restricted CD8+ Cytotoxic T Lymphocyte Epitopes Identified from Herpes Simplex Virus Glycoprotein D1 , 2008, The Journal of Immunology.