An Overview of Bioinformatics Tools and Resources in Allergy.
暂无分享,去创建一个
[1] M. Lefranc. IMGT, the International ImMunoGeneTics Information System. , 2011, Cold Spring Harbor protocols.
[2] Adriano Mari,et al. Bioinformatics applied to allergy: allergen databases, from collecting sequence information to data integration. The Allergome platform as a model. , 2006, Cellular immunology.
[3] Bo Yao,et al. Conformational B-Cell Epitope Prediction on Antigen Protein Structures: A Review of Current Algorithms and Comparison with Common Binding Site Prediction Methods , 2013, PloS one.
[4] Manoj Bhasin,et al. Prediction of promiscuous and high-affinity mutated MHC binders. , 2003, Hybridoma and hybridomics.
[5] M. Levitt. Conformational preferences of amino acids in globular proteins. , 1978, Biochemistry.
[6] E. Reinherz,et al. Prediction of peptide-MHC binding using profiles. , 2007, Methods in molecular biology.
[7] O. Schueler‐Furman,et al. Structure‐based prediction of binding peptides to MHC class I molecules: Application to a broad range of MHC alleles , 2000, Protein science : a publication of the Protein Society.
[8] Mathias M Schuler,et al. SYFPEITHI: database for searching and T-cell epitope prediction. , 2007, Methods in molecular biology.
[9] Pierre Baldi,et al. PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure , 2008, Bioinform..
[10] Channa K. Hattotuwagama,et al. AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data , 2005, Immunome research.
[11] Yuxin Li,et al. Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis , 2008, BMC Bioinformatics.
[12] Sneh Lata,et al. TAPPred prediction of TAP-binding peptides in antigens. , 2007, Methods in molecular biology.
[13] Oliver Kohlbacher,et al. SVMHC: a server for prediction of MHC-binding peptides , 2006, Nucleic Acids Res..
[14] Channa K. Hattotuwagama,et al. MHCPred 2.0: an updated quantitative T-cell epitope prediction server. , 2006, Applied bioinformatics.
[15] Anne S De Groot,et al. Immunomics: discovering new targets for vaccines and therapeutics. , 2006, Drug discovery today.
[16] H. Rammensee,et al. SYFPEITHI: database for MHC ligands and peptide motifs , 1999, Immunogenetics.
[17] Fu Zhi. Construction and Application of a Large Scale cDNA Sequences Analysis System Based on Unix , 2002 .
[18] Morten Nielsen,et al. NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11 , 2008, Nucleic Acids Res..
[19] Zhiqiang Ma,et al. Bioinformatics Resources and Tools for Conformational B-Cell Epitope Prediction , 2013, Comput. Math. Methods Medicine.
[20] Pingping Guan,et al. EpiJen: a server for multistep T cell epitope prediction , 2006, BMC Bioinformatics.
[21] Werner Braun,et al. Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences , 2009, Bioinformatics and biology insights.
[22] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[23] Minoru Kanehisa,et al. MIMOX: a web tool for phage display based epitope mapping , 2006, BMC Bioinformatics.
[24] H. Sampson,et al. Is epitope recognition of shrimp allergens useful to predict clinical reactivity? , 2012, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.
[25] Ulf Leser,et al. Systematic feature evaluation for gene name recognition , 2005, BMC Bioinformatics.
[26] Gajendra P. S. Raghava,et al. Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences , 2005, Nucleic Acids Res..
[27] Gajendra P. S. Raghava,et al. ProPred: prediction of HLA-DR binding sites , 2001, Bioinform..
[28] Nimrod D. Rubinstein,et al. Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm , 2006, Nucleic acids research.
[29] 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.
[30] Kun Yu,et al. Methods for Prediction of Peptide Binding to MHC Molecules: A Comparative Study , 2002, Molecular medicine.
[31] Wei Zhang,et al. SEPPA 2.0—more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen , 2014, Nucleic Acids Res..
[32] Bo Yao,et al. EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results , 2010, BMC Bioinformatics.
[33] Violaine Moreau,et al. Discontinuous epitope prediction based on mimotope analysis , 2006, Bioinform..
[34] Morten Nielsen,et al. Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction , 2007, BMC Bioinformatics.
[35] R. Hodges,et al. New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. , 1986, Biochemistry.
[36] Ping Zhu,et al. MimoDB 2.0: a mimotope database and beyond , 2011, Nucleic Acids Res..
[37] E. Emini,et al. Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide , 1985, Journal of virology.
[38] Didier Rognan,et al. Recovery of known T-cell epitopes by computational scanning of a viral genome , 2002, J. Comput. Aided Mol. Des..
[39] P. Y. Chou,et al. Prediction of the secondary structure of proteins from their amino acid sequence. , 2006 .
[40] C. Akdis,et al. Immunological mechanisms of allergen‐specific immunotherapy , 2011, Allergy.
[41] Luciano Milanesi,et al. ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro , 2002, Nucleic Acids Res..
[42] O. Lund,et al. NetMHCpan, a method for MHC class I binding prediction beyond humans , 2008, Immunogenetics.
[43] Darren R Flower,et al. Proteomics in Vaccinology and Immunobiology: An Informatics Perspective of the Immunone , 2003, Journal of biomedicine & biotechnology.
[44] Channa K. Hattotuwagama,et al. MHCPred 2.0 , 2006 .
[45] Morten Nielsen,et al. Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking , 2012, PLoS Comput. Biol..
[46] Ping Dai,et al. Bioinformatics Resources and Tools for Phage Display , 2011, Molecules.
[47] Jing Wang,et al. Evaluation and integration of existing methods for computational prediction of allergens , 2013, BMC Bioinformatics.
[48] Michael B. Stadler,et al. Allergenicity prediction by protein sequence , 2003, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[49] J. McCluskey,et al. Drug hypersensitivity and human leukocyte antigens of the major histocompatibility complex. , 2012, Annual review of pharmacology and toxicology.
[50] Shi-cui Zhang,et al. EST analysis of mRNAs expressed in neurula of Chinese amphioxus. , 2002, Biochemical and biophysical research communications.
[51] Itay Mayrose,et al. Epitopia: a web-server for predicting B-cell epitopes , 2009, BMC Bioinformatics.
[52] V Brusic,et al. Computational tools for the study of allergens , 2003, Allergy.
[53] Avner Schlessinger,et al. Towards a consensus on datasets and evaluation metrics for developing B‐cell epitope prediction tools , 2007, Journal of molecular recognition : JMR.
[54] Morten Nielsen,et al. Improved method for predicting linear B-cell epitopes , 2006, Immunome research.
[55] Chi Zhang,et al. Prediction of antigenic epitopes on protein surfaces by consensus scoring , 2009, BMC Bioinformatics.
[56] Roded Sharan,et al. BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btm493 Structural bioinformatics Pepitope: epitope mapping from affinity-selected peptides , 2022 .
[57] M. Bhasin,et al. Bcipep: A database of B-cell epitopes , 2005, BMC Genomics.
[58] 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.
[59] Morten Nielsen,et al. NetCTLpan: pan-specific MHC class I pathway epitope predictions , 2010, Immunogenetics.
[60] P. Dönnes,et al. Integrated modeling of the major events in the MHC class I antigen processing pathway , 2005, Protein science : a publication of the Protein Society.
[61] 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.
[62] Hasan H. Otu,et al. Prediction of peptides binding to MHC class I and II alleles by temporal motif mining , 2013, BMC Bioinformatics.
[63] Deborah Hix,et al. The immune epitope database (IEDB) 3.0 , 2014, Nucleic Acids Res..
[64] E Westhof,et al. Predicting location of continuous epitopes in proteins from their primary structures. , 1991, Methods in enzymology.
[65] Tatsuya Akutsu,et al. Protein homology detection using string alignment kernels , 2004, Bioinform..
[66] Werner Braun,et al. SDAP: database and computational tools for allergenic proteins , 2003, Nucleic Acids Res..
[67] Vasant Honavar,et al. Recent advances in B-cell epitope prediction methods , 2010, Immunome research.
[68] Yasser Mohamed El-manzalawy,et al. Machine learning approaches for epitope prediction , 2008 .
[69] Yang Lu,et al. MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries , 2011, BMC Bioinformatics.
[70] O. Lund,et al. Prediction of residues in discontinuous B‐cell epitopes using protein 3D structures , 2006, Protein science : a publication of the Protein Society.
[71] Anthony Kusalik,et al. Strength in numbers: achieving greater accuracy in MHC-I binding prediction by combining the results from multiple prediction tools , 2007, Immunome research.
[72] K. R. Woods,et al. Prediction of protein antigenic determinants from amino acid sequences. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[73] A S Kolaskar,et al. Prediction of three-dimensional structure and mapping of conformational epitopes of envelope glycoprotein of Japanese encephalitis virus. , 1999, Virology.
[74] Yongchao Ge,et al. Development of a novel peptide microarray for large-scale epitope mapping of food allergens. , 2009, The Journal of allergy and clinical immunology.
[75] Gajendra P. S. Raghava,et al. AlgPred: prediction of allergenic proteins and mapping of IgE epitopes , 2006, Nucleic Acids Res..
[76] Gajendra P.S. Raghava,et al. Prediction of CTL epitopes using QM, SVM and ANN techniques. , 2004, Vaccine.
[77] K. Dyer,et al. Eosinophil cationic protein and eosinophil-derived neurotoxin. Evolution of novel function in a primate ribonuclease gene family. , 1995, The Journal of biological chemistry.
[78] Urmila Kulkarni-Kale,et al. CEP: a conformational epitope prediction server , 2005, Nucleic Acids Res..
[79] 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.
[80] K. Hadeler,et al. PAProC: a prediction algorithm for proteasomal cleavages available on the WWW , 2001, Immunogenetics.
[81] Wei Li,et al. ElliPro: a new structure-based tool for the prediction of antibody epitopes , 2008, BMC Bioinformatics.
[82] R. Aalberse,et al. Structural biology of allergens. , 2000, The Journal of allergy and clinical immunology.
[83] S. Tanabe. Epitope peptides and immunotherapy. , 2007, Current protein & peptide science.
[84] Daniel Soeria-Atmadja,et al. Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteins , 2005, Bioinform..
[85] C. Radauer,et al. Update of the WHO/IUIS Allergen Nomenclature Database based on analysis of allergen sequences , 2014, Allergy.
[86] Timur Shtatland,et al. PepBank - a database of peptides based on sequence text mining and public peptide data sources , 2007, BMC Bioinformatics.
[87] Jérôme Lane,et al. IMGT®, the international ImMunoGeneTics information system® , 2004, Nucleic Acids Res..
[88] James Robinson,et al. The IMGT/HLA database , 2008, Nucleic Acids Res..
[89] Yang Dai,et al. Prediction of MHC class II binding peptides based on an iterative learning model , 2005, Immunome research.
[90] A. Boner,et al. A bioinformatics approach to identify patients with symptomatic peanut allergy using peptide microarray immunoassay. , 2012, The Journal of allergy and clinical immunology.
[91] Y. Z. Chen,et al. Prediction of MHC-binding peptides of flexible lengths from sequence-derived structural and physicochemical properties. , 2007, Molecular immunology.
[92] Itay Mayrose,et al. Stepwise prediction of conformational discontinuous B‐cell epitopes using the Mapitope algorithm , 2007, Proteins.
[93] Johannes Söllner,et al. Selection and combination of machine learning classifiers for prediction of linear B‐cell epitopes on proteins , 2006, Journal of molecular recognition : JMR.
[94] Sudipto Saha,et al. Prediction of continuous B‐cell epitopes in an antigen using recurrent neural network , 2006, Proteins.