PREDTAPserver
[http://antigen.i2r.a-star.edu.sg/predTAP]
Cresswell P, Ackerman AL, Giodini A, Peaper DR, Wearsch PA: Mechanisms of MHC class I-restricted antigen processing and cross-presentation.
Immunol Rev 2005, 207:145–157.
Article
CAS
PubMed
Google Scholar
Strehl B, Seifert U, Kruger E, Heink S, Kuckelkorn U, Kloetzel PM: Interferon-gamma, the functional plasticity of the ubiquitin-proteasome system, and MHC class I antigen processing.
Immunol Rev 2005, 207:19–30.
Article
CAS
PubMed
Google Scholar
Saveanu L, Carroll O, Hassainya Y, van Endert P: Complexity, contradictions, and conundrums: studying post-proteasomal proteolysis in HLA class I antigen presentation.
Immunol Rev 2005, 207:42–59.
Article
CAS
PubMed
Google Scholar
Abele R, Tampe R: Function of the transport complex TAP in cellular immune recognition.
Biochim Biophys Acta 1999, 1461:405–419.
Article
CAS
PubMed
Google Scholar
Abele R, Tampe R: Modulation of the antigen transport machinery TAP by friends and enemies.
FEBS Lett 2006, 580:1156–1163.
Article
CAS
PubMed
Google Scholar
van Endert PM, Riganelli D, Greco G, Fleischhauer K, Sidney J, Sette A, Bach JF: The peptide-binding motif for the human transporter associated with antigen processing.
J Exp Med 1995, 182:1883–1895.
Article
CAS
PubMed
Google Scholar
Nijenhuis M, Schmitt S, Armandola EA, Obst R, Brunne J, Hammerling GJ: Identification of a contact region for peptide on the TAP1 chain of the transporter associated with antigen processing.
J Immunol 1996, 156:2186–2195.
CAS
PubMed
Google Scholar
Gadola SD, Moins-Teisserenc HT, Trowsdale J, Gross WL, Cerundolo V: TAP deficiency syndrome.
Clin Exp Immunol 2000, 121:173–178.
Article
CAS
PubMed
Google Scholar
Smith KD, Lutz CT: Peptide-dependent expression of HLA-B7 on antigen processing-deficient T2 cells.
J Immunol 1996, 156:3755–3764.
CAS
PubMed
Google Scholar
Brusic V, Bajic VB, Petrovsky N: Computational methods for prediction of T-cell epitopes – a framework for modelling, testing, and applications.
Methods 2004, 34:436–43.
Article
CAS
PubMed
Google Scholar
Daniel S, Brusic V, Caillat-Zucman S, Petrovsky N, Harrison L, Riganelli D, Sinigaglia F, Gallazzi F, Hammer J, van Endert PM: Relationship between peptide selectivities of human transporters associated with antigen processing and HLA class I molecules.
J Immunol 1998, 161:617–624.
CAS
PubMed
Google Scholar
Peters B, Bulik S, Tampe R, Van Endert PM, Holzhutter HG: Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors.
J Immunol 2003, 171:1741–1749.
CAS
PubMed
Google Scholar
Doytchinova I, Hemsley S, Flower DR: Transporter associated with antigen processing preselection of peptides binding to the MHC: a bioinformatic evaluation.
J Immunol 2004, 173:6813–6819.
CAS
PubMed
Google Scholar
Brusic V, van Endert P, Zeleznikow J, Daniel S, Hammer J, Petrovsky N: A neural network model approach to the study of human TAP transporter.
In Silico Biol 1999, 1:109–121.
CAS
PubMed
Google Scholar
Bhasin M, Raghava GP: Analysis and prediction of affinity of TAP binding peptides using cascade SVM.
Protein Sci 2004, 13:596–607.
Article
CAS
PubMed
Google Scholar
Petrovsky N, Brusic V: Virtual models of the HLA class I antigen processing pathway.
Methods 2004, 34:429–35.
Article
CAS
PubMed
Google Scholar
Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M: An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions.
Eur J Immunol 2005, 35:2295–2303.
Article
CAS
PubMed
Google Scholar
Donnes P, Kohlbacher O: Integrated modeling of the major events in the MHC class I antigen processing pathway.
Protein Sci 2005, 14:2132–2140.
Article
PubMed
Google Scholar
Peters B, Sette A: Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method.
BMC Bioinformatics 2005, 6:132.
Article
PubMed
Google Scholar
Tenzer S, Peters B, Bulik S, Schoor O, Lemmel C, Schatz MM, Kloetzel PM, Rammensee HG, Schild H, Holzhutter HG: Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding.
Cell Mol Life Sci 2005, 62:1025–1037.
Article
CAS
PubMed
Google Scholar
Doytchinova IA, Guan P, Flower DR: EpiJen: a server for multistep T cell epitope prediction.
BMC Bioinformatics 2006, 7:131.
Article
PubMed
Google Scholar
Groothuis TA, Griekspoor AC, Neijssen JJ, Herberts CA, Neefjes JJ: MHC class I alleles and their exploration of the antigen-processing machinery.
Immunol Rev 2005, 207:60–76.
Article
CAS
PubMed
Google Scholar
Lautscham G, Mayrhofer S, Taylor G, Haigh T, Leese A, Rickinson A, Blake N: Processing of a multiple membrane spanning Epstein-Barr virus protein for CD8(+) T cell recognition reveals a proteasome-dependent, transporter associated with antigen processing-independent pathway.
J Exp Med 2001, 194:1053–1068.
Article
CAS
PubMed
Google Scholar
Zimmer J, Andres E, Donato L, Hanau D, Hentges F, de la Salle H: Clinical and immunological aspects of HLA class I deficiency.
QJM 2005, 98:719–727.
Article
CAS
PubMed
Google Scholar
Brusic V, Petrovsky N, Zhang G, Bajic VB: Prediction of promiscuous peptides that bind HLA class I molecules.
Immunol Cell Biol 2002, 80:280–285.
Article
CAS
PubMed
Google Scholar
Udaka K, Mamitsuka H, Nakaseko Y, Abe N: Empirical evaluation of a dynamic experiment design method for prediction of MHC class I-binding peptides.
J Immunol 2002, 169:5744–5753.
CAS
PubMed
Google Scholar
Zhang P: Model selection via multifold cross validation.
Ann Stat 1993, 21:299–313.
Article
Google Scholar
Swets JA: Measuring the accuracy of diagnostic systems.
Science 1988, 240:1285–1293.
Article
CAS
PubMed
Google Scholar
Kast WM, Brandt RM, Sidney J, Drijfhout JW, Kubo RT, Grey HM, Melief CJ, Sette A: Role of HLA-A motifs in identification of potential CTL epitopes in human papillomavirus type 16 E6 and E7 proteins.
J Immunol 1994, 152:3904–3912.
CAS
PubMed
Google Scholar
Monji M, Nakatsura T, Senju S, Yoshitake Y, Sawatsubashi M, Shinohara M, Kageshita T, Ono T, Inokuchi A, Nishimura Y: Identification of a novel human cancer/testis antigen, KM-HN-1, recognized by cellular and humoral immune responses.
Clin Cancer Res 2004, 10:6047–6057.
Article
CAS
PubMed
Google Scholar
Smith KD, Lutz CT: Peptide-dependent expression of HLA-B7 on antigen processing-deficient T2 cells.
J Immunol 1996, 156:3755–3764.
CAS
PubMed
Google Scholar
Neisig A, Roelse J, Sijts A, Ossendorp F, Feltkamp M, Kast W, Melief C, Neefjes J: Major differences in transporter associated with antigen presentation (TAP)-dependent translocation of MHC class I-presentable peptides and the effect of flanking sequences.
J Immunol 1995, 154:1273–1279.
CAS
PubMed
Google Scholar
Brusic V, Petrovsky N: Immunoinformatics and its relevance to understanding human immune disease.
Expert Rev Clin Immunol 2005, 1:145–157.
Article
CAS
PubMed
Google Scholar