Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan

PLoS Computational Biology

Volumn 4, Issue 7, 2008, Pages

  Nielsen, Morten ^a   Lundegaard, Claus ^a   Blicher, Thomas ^a   Peters, Bjoern ^b   Sette, Alessandro ^b   Justesen, Sune ^c   Buus, Søren ^c   Lund, Ole ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b LA JOLLA INSTITUTE FOR ALLERGY AND IMMUNOLOGY   (United States)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPES; FORECASTING; GENES; ITERATIVE METHODS; PEPTIDES;

CELL CONTROL; CELL-BE; CELL/B.E; CELL/BE; CLASS II; MAJOR HISTOCOMPATIBILITY COMPLEX; MAJOR HISTOCOMPATIBILITY COMPLEX CLASS; PEPTIDE BINDING; PROTEIN ANTIGENS; QUANTITATIVE PREDICTION;

MOLECULES;

HLA DR ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2;

ALLELE; ANTIGEN BINDING; ARTICLE; CD4+ T LYMPHOCYTE; HUMAN; PEPTIDE ANALYSIS; PREDICTION; PROTEIN BINDING; QUANTITATIVE ANALYSIS; VALIDATION STUDY; ALGORITHM; AMINO ACID SEQUENCE; BINDING SITE; GENETICS; IMMUNOLOGY; MAJOR HISTOCOMPATIBILITY COMPLEX; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PHYSIOLOGY; PREDICTION AND FORECASTING; PROTEIN ANALYSIS; PROTEIN DATABASE; REPRODUCIBILITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; ALLELES; AMINO ACID SEQUENCE; BINDING SITES; DATABASES, PROTEIN; HLA-DR ANTIGENS; HUMANS; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR SEQUENCE DATA; PREDICTIVE VALUE OF TESTS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 48249083459     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000107     Document Type: Article

References (41)

1. Castellino F, Zhong G, Germain RN (1997) Antigen presentation by MHC class II molecules: invariant chain function, protein trafficking, and the molecular basis of diverse determinant capture. Hum Immunol 54: 159-169.
2. Robinson J, Waller MJ, Parham P, Bodmer JG, Marsh SGE (2001) IMGT/HLA Database - a sequence database for the human major histocompatibility complex. Nucleic Acids Res 29: 210-213.
3. Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, et al. (2007) NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS ONE 2: e796. doi:10.1371/journal.pone.0000796.
4. Sette A, Peters B (2007) Immune epitope mapping in the post-genomic era: lessons for vaccine development. Curr Opin Immunol 19: 106-110.
5. Lauemoller SL, Kesmir C, Corbet SL, Fomsgaard A, Holm A, et al. (2000) Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project." Rev Immunogenet 2: 477-491.
6. Moutaftsi M, Peters B, Pasquetto V, Tscharke DC, Sidney J, et al. (2006) A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus. Nat Biotechnol 24: 817-819.
7. Yewdell JW, Bennink JR (1999) Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses. Annu Rev Immunol 17: 51-88.
8. Haque A, Blum JS (2005) New insights in antigen processing and epitope selection: development of novel immunotherapeutic strategies for cancer, autoimmunity and infectious diseases. J Biol Regul Homeost Agents 19: 93-104.
9. Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M (2007) Modeling the adaptive immune system: predictions and simulations. Bioinformatics 23: 3265-3275.
10. Sylvester-Hvid C, Kristensen N, Blicher T, Ferré H, Lauemøller SL, et al. (2002) Establishment of a quantitative ELISA capable of determining peptide - MHC class I interaction. Tissue Antigens 59: 251-258.
11. Nielsen M, Lundegaard C, Worning P, Lauemoller SL, Lamberth K, et al. (2003) Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci 12: 1007-1017.
12. Peters B, Bui HH, Frankild S, Nielson M, Lundegaard C, et al. (2006) A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol 2: e65. doi: 10.1371/journal.pcbi.0020065.
13. Karpenko O, Shi J, Dai Y (2005) Prediction of MHC class II binders using the ant colony search strategy. Artif Intell Med 35: 147-156.
14. Murugan N, Dai Y (2005) Prediction of MHC class II binding peptides based on an iterative learning model. Immunome Res 1: 6.
15. Chang ST, Ghosh D, Kirschner DE, Linderman JJ (2006) Peptide length-based prediction of peptide-MHC class II binding. Bioinformatics 22: 2761-2767.
16. Salomon J, Flower DR (2006) Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores. BMC Bioinformatics 7: 501.
17. Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A, et al. (2005) Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics 57: 304-314.
18. Nielsen M, Lundegaard C, Worning P, Hvid CS, Lamberth K, et al. (2004) Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics 20: 1388-1397.
19. Wan J, Liu W, Xu Q, Ren Y, Flower DR, et al. (2006) SVRMHC prediction server for MHC-binding peptides. BMC Bioinformatics 7: 463.
20. Brusic V, Rudy G, Honeyman G, Hammer J, Harrison L (1998) Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network. Bioinformatics 14: 121-130.
21. Noguchi H, Kato R, Hanai T, Matsubara Y, Honda H, et al. (2002) Hidden Markov model-based prediction of antigenic peptides that interact with MHC class II molecules. J Biosci Bioeng 94: 264-270.
22. Rajapakse M, Schmidt B, Feng L, Brusic V (2007) Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms. BMC Bioinformatics 8: 459.
23. Doytchinova IA, Flower DR (2003) Towards the in silico identification of class II restricted T-cell epitopes: a partial least squares iterative self-consistent algorithm for affinity prediction. Bioinformatics 19: 2263-2270.
24. Cui J, Han LY, Lin HH, Zhang HL, Tang ZQ, et al. (2007) Prediction of MHC-binding peptides of flexible lengths from sequence-derived structural and physicochemical properties. Mol Immunol 44: 866-877.
25. Singh H, Raghava GP (2001) ProPred: prediction of HLA-DR binding sites. Bioinformatics 17: 1236-1237.
26. Nielsen M, Lundegaard C, Lund O (2007) Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics 8: 238.
27. Sturniolo T, Bono E, Ding J, Raddrizzani L, Tuereci O, et al. (1999) Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat Biotechnol 17: 555-561.
28. Sette A, Fleri W, Peters B, Sathiamurthy M, Bui HH, et al. (2005) A roadmap for the immunomics of category A-C pathogens. Immunity 22: 155-161.
29. Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S (1999) SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50: 213-219.
30. Sette A, Adorini L, Appella E, Colon SM, Miles C, et al. (1989) Structural requirements for the interaction between peptide antigens and I-Ed molecules. J Immunol 143: 3289-3294.
31. Swets JA (1988) Measuring the accuracy of diagnostic systems. Science 240: 1285-1293.
32. Press WH, Flannery BP, Teukolsky SA, Vetterling WT (1992) Numerical Recipies in C: The Art of Scientific Computing. Cambridge: Cambridge University Press.
33. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31: 365-370.
34. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, et al. (2002) The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 58: 899-907.
35. Lund O, Nielsen M, Kesmir C, Petersen AG, Lundegaard C, et al. (2004) Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics 55: 797-810.
36. Middleton D, Menchaca L, Rood H, Komerofsky R (2003) New allele frequency database: http://www.allelefrequencies.net. Tissue Antigens 61: 403-407.
37. Alexander J, Sidney J, Southwood S, Ruppert J, Oseroff C, et al. (1994) Development of high potency universal DR-restricted helper epitopes by modification of high affinity DR-blocking peptides. Immunity 1: 751-761.
38. Christensen JK, Lamberth K, Nielsen M, Lundegaard C, Worning P, et al. (2003) Selecting informative data for developing peptide-MHC binding predictors using a query by committee approach. Neural Comput 15: 2931-2942.
39. Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89: 10915-10919.
40. Hobohm U, Scharf M, Schneider R, Sander C (1992) Selection of representative protein data sets. Protein Sci 1: 409-417.
41. Gauthier L, Smith KJ, Pyrdol J, Kalandadze A, Strominger JL, et al. (1998) Expression and crystallization of the complex of HLA-DR2 (DRA, DRB1*1501) and an immunodominant peptide of human myelin basic protein. Proc Natl Acad Sci U S A 95: 11828-11833.