An effective and effecient peptide binding prediction approach for a broad set of HLA-DR molecules based on ordered weighted averaging of binding pocket profiles

Proteome Science

Volumn 11, Issue , 2013, Pages

  Shen, Wen Jun ^a   Zhang, Shaohong ^b   Wong, Hau San ^a  

^a CITY UNIVERSITY OF HONG KONG   (Hong Kong)

^b GUANGZHOU UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

HLA DR ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2;

ALGORITHM; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANTIGEN BINDING; ANTIGEN STRUCTURE; ARTICLE; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; IMMUNE SYSTEM; LIGAND BINDING; ORDERED WEIGHTED AVERAGING; OWA-PSSM; PREDICTION; PROBABILITY; PROTEIN BINDING; QUANTITATIVE ANALYSIS; RADIAL BASED FUNCTION; SCORING SYSTEM; STATISTICAL ANALYSIS; TEPITOPE; X RAY CRYSTALLOGRAPHY;

EID: 84988355032     PISSN: None     EISSN: 14775956     Source Type: Journal    
DOI: 10.1186/1477-5956-11-S1-S15     Document Type: Article

References (34)

1. Kindt TJ, Goldsby RA, Osborne BA, Kuby J: Kuby immunology WH Freeman & Company; 2007.
2. Germain R: MHC-dependent antigen processing and peptide presentation: providing ligands for T lymphocyte activation. Cell 1994, 76(2):287-299.
3. Lund O: Immunological Bioinformatics The MIT Press; 2005.
4. Sette A, Adorini L, Appella E, Colon S, Miles C, Tanaka S, Ehrhardt C, Doria G, Nagy Z, Buus S: Structural requirements for the interaction between peptide antigens and I-Ed molecules. The Journal of Immunology 1989, 143(10):3289-3294.
5. Rammensee H, Bachmann J, Emmerich N, Bachor O, Stevanovi´c S: SYFPEITHI: database for MHC ligands and peptide motifs.Immunogenetics 1999, 50(3):213-219.
6. Kropshofer H, Max H, Halder T, Kalbus M, Muller C, Kalbacher H: Selfpeptides from four HLA-DR alleles share hydrophobic anchor residues near the NH2-terminal including proline as a stop signal for trimming. The Journal of Immunology 1993, 151(9):4732-4742.
7. Nielsen M, Lundegaard C, Lund O: Prediction of MHC class II binding affenity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics 2007, 8:238.
8. Lin H, Ray S, Tongchusak S, Reinherz E, Brusic V: Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. BMC Immunology 2008, 9:8.
9. Zhang L, Chen Y, Wong H, Zhou S, Mamitsuka H, Zhu S: TEPITOPEpan: Extending TEPITOPE for Peptide Binding Prediction Covering over 700 HLA-DR Molecules. PloS ONE 2012, 7(2):e30483.
10. Sturniolo T, Bono E, Ding J, Raddrizzani L, Tuereci O, Sahin U, Braxenthaler M, Gallazzi F, Protti M, Sinigaglia F, et al: Generation of tissuespecific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nature Biotechnology 1999, 17(6):555-561.
11. Pfeifer N, Kohlbacher O: Multiple instance learning allows MHC class II epitope predictions across alleles. Algorithms in Bioinformatics 2008, 5251:210-221.
12. Nielsen M, Lundegaard C, Blicher T, Peters B, Sette A, Justesen S, Buus S, Lund O: Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan. PLoS Computational Biology 2008, 4(7):e1000107.
13. Bordner A, Mittelmann H: MultiRTA: A simple yet reliable method for predicting peptide binding affenities for multiple class II MHC allotypes. BMC Bioinformatics 2010, 11:482.
14. Nielsen M, Justesen S, Lund O, Lundegaard C, Buus S: NetMHCIIpan-2.0-Improved pan-specific HLADR predictions using a novel concurrent alignment and weight optimization training procedure. Immunome Research 2010, 6:9.
15. Nielsen M, Lund O: NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics 2009, 10:296.
16. Zhang G, DeLuca D, Keskin D, Chitkushev L, Zlateva T, Lund O, Reinherz E, Brusic V: MULTIPRED2: A computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles. Journal of Immunological Methods 2011, 374:53-61.
17. Zhang H, Lund O, Nielsen M: The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding. Bioinformatics 2009, 25(10):1293-1299.
18. Shen WJ, Wong HS: OWA-PSSM-A position specific scoring matrix based method integrated with OWA weights for HLA-DR peptide binding prediction. BIBM 2012 2012, doi:10.1109/BIBM.2012.6392705.
19. Yager R: On ordered weighted averaging aggregation operators in multicriteria decisionmaking. IEEE Transactions on Systems, Man, and Cybernetics 1988, 18:183-190.
20. Filev D, Yager R: On the issue of obtaining OWA operator weights. Fuzzy Sets and Systems 1998, 94(2):157-169.
21. Sadiq R, Tesfamariam S: Probability density functions based weights for ordered weighted averaging (OWA) operators: an example of water quality indices. European Journal of Operational Research 2007, 182(3):1350-1368.
22. Raghava G: MHCBench: Evaluation of MHC Binding Peptide Prediction Algorithms. 2006 [http://www.imtech.res.in/raghava/mhcbench].
23. Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H, Shindyalov I, Bourne P: The protein data bank. Nucleic Acids Research 2000, 28:235-242.
24. Kaas Q, Ruiz M, Lefranc M: IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic acids research 2004, 32(1): D208-D210.
25. Reche P, Glutting J, Reinherz E: Prediction of MHC class I binding peptides using profile motifs. Human Immunology 2002, 63(9):701-709.
26. Reche P, Glutting J, Zhang H, Reinherz E: Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles. Immunogenetics 2004, 56(6):405-419.
27. Reche P, Zhang H, Glutting J, Reinherz E: EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology. Bioinformatics 2005, 21(9):2140-2141.
28. Reche P, Reinherz E: Prediction of peptide-MHC binding using profiles. Methods in Molecular Biology 2007, 409:185.
29. Singh H, Raghava G: ProPred: prediction of HLA-DR binding sites. Bioinformatics 2001, 17(12):1236-1237.
30. Henikoff S, Henikoff J: Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences 1992, 89(22):10915.
31. Kawashima S, Kanehisa M: AAindex: amino acid index database. Nucleic Acids Research 2000, 28:374-374.
32. McLachlan A: Repeating sequences and gene duplication in proteins. Journal of molecular biology 1972, 64(2):417-437.
33. Hammer J, Bono E, Gallazzi F, Belunis C, Nagy Z, Sinigaglia F: Precise prediction of major histocompatibility complex class II-peptide interaction based on peptide side chain scanning. The Journal of Experimental Medicine 1994, 180(6):2353.
34. Nielsen M, Lundegaard C, Worning P, Hvid C, Lamberth K, Buus S, Brunak S, Lund O: Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics 2004, 20(9):1388-1397.