Immunogenicity screening in protein drug development

Bibliography

• LOCATELLI F, DEL VECCHIO L: Pure red cell aplasia secondary to treatment with erythropoietin. J. Nephrol. (2003) 16:461-466.
   PubMed Web of Science ®Google Scholar
• MIRE-SLUIS AR, BARRETT YC, DEVANARAYAN V et al.: Recommendations for the design and optimization of immunoassays used in the detection of host antibodies against biotechnology products. J. Immunol. Methods (2004) 289:1-16.
   PubMed Web of Science ®Google Scholar
• BEARDEN CM, BOOK BK, SIDNER RA, PESCOVITZ MD: Removal of therapeutic anti-lymphocyte antibodies from human sera prior to anti-human leukocyte antibody testing. J. Immunol. Methods (2005) 300:192-199.
   PubMed Web of Science ®Google Scholar
• PATTON A, MULLENIX MC, SWANSON SJ, KOREN E: An acid dissociation bridging ELISA for detection of antibodies directed against therapeutic proteins in the presence of antigen. J. Immunol. Methods (2005) 304:189-195.
   PubMed Web of Science ®Google Scholar
• MCINTYRE JA, KINCADE M, HIGGINS NG: Detection of IGA anti-OKT3 antibodies in OKT3-treated transplant recipients. Transplantation (1996) 61(10):1465-1469.
   PubMed Web of Science ®Google Scholar
• UCKUN FM, MESSINGER Y, CHEN CL et al.: Treatment of therapy-refractory B-lineage acute lymphoblastic leukemia with an apoptosis-inducing CD19-directed tyrosine kinase inhibitor. Clin. Cancer Res. (1999) 5(12):3906-3913.
   PubMed Web of Science ®Google Scholar
• KAMINSKI MS, ZELENETZ AD, PRESS OW et al.: Pivotal study of iodine I 131 tositumomab for chemotherapy-refractory low-grade or transformed low-grade B-cell non-Hodgkin’s lymphomas. J. Clin. Oncol. (2001) 19(19):3918-3928.
   PubMed Web of Science ®Google Scholar
• STROOMER JW, ROOS JC, SPROLL M et al.: Safety and biodistribution of 99mTechnetium-labeled anti-CD44v6 monoclonal antibody BIWA 1 in head and neck cancer patients. Clin. Cancer Res. (2000) 6(8):3046-3055.
   PubMed Web of Science ®Google Scholar
• KOVARIK J, WOLF P, CISTERNE JM et al.: Disposition of basiliximab, an interleukin-2 receptor monoclonal antibody, in recipients of mismatched cadaver renal allografts. Transplantation (1997) 64(12):1701-1705.
   PubMed Web of Science ®Google Scholar
• TCHENG JE, KEREIAKES DJ, LINCOFF AM et al.: Abciximab readministration: results of the ReoPro Readministration Registry. Circulation (2001) 104(8):870-875.
   PubMed Web of Science ®Google Scholar
• HANAUER SB: Review article: safety of infliximab in clinical trials. Aliment. Pharmacol. Ther. (1999) 13(Suppl. 4):16-22.
   PubMed Web of Science ®Google Scholar
• BAERT F, NOMAN M, VERMEIRE S et al.: Influence of immunogenicity on the long-term efficacy of infliximab in Crohn’s disease. N. Engl. J. Med. (2003) 348(7):601-608.
   PubMed Web of Science ®Google Scholar
• LIPSKY PE, VAN DER HEIJDE DM, ST CLAIR EW et al.: Infliximab and methotrexate in the treatment of rheumatoid arthritis. Anti-Tumor Necrosis Factor Trial in Rheumatoid Arthritis with Concomitant Therapy Study Group. N. Engl. J. Med. (2000) 343(22):1594-1602.
   PubMed Web of Science ®Google Scholar
• DAVIS TA, GRILLO-LÓPEZ AJ, WHITE CA et al.: Rituximab anti-CD20 monoclonal antibody therapy in non-Hodgkin’s lymphoma: safety and efficacy of re-treatment. J. Clin. Oncol. (2000) 18(17):3135-3143.
   PubMed Web of Science ®Google Scholar
• PIRO LD, WHITE CA, GRILLO-LÓPEZ AJ et al.: Extended Rituximab (anti-CD20 monoclonal antibody) therapy for relapsed or refractory low-grade or follicular non-Hodgkin’s lymphoma. Ann. Oncol. (1999) 10(6):655-661.
   PubMed Web of Science ®Google Scholar
• LOONEY RJ, ANOLIK JH, CAMPBELL D et al.: B cell depletion as a novel treatment for systemic lupus erythematosus: a Phase I/II dose-escalation trial of rituximab. Arthritis Rheum. (2004) 50(8):2580-2589.
   PubMed Web of Science ®Google Scholar
• PIJPE J, VAN IMHOFF GW, SPIJKERVET FK et al.: Rituximab treatment in patients with primary Sjögren’s syndrome: an open-label Phase II study. Arthritis Rheum. (2005) 52(9):2740-2750.
   PubMed Web of Science ®Google Scholar
• BAERT F, NOMAN M, VERMEIRE S et al.: Influence of immunogenicity on the long-term efficacy of infliximab in Crohn’s disease. N. Engl. J. Med. (2003) 348(7):601-608.
   PubMed Web of Science ®Google Scholar
• HANDGRETINGER R, ANDERSON K, LANG P et al.: A Phase I study of human/mouse chimeric antiganglioside GD2 antibody ch14.18 in patients with neuroblastoma. Eur. J. Cancer (1995) 31A(2):261-267.
   PubMed Web of Science ®Google Scholar
• SAWADA T, NISHIHARA T, YAMAMOTO A et al.: Preoperative clinical radioimmunodetection of pancreatic cancer by 111 In-labeled chimeric monoclonal antibody Nd2. Jpn. J. Cancer Res. (1999) 90(10):1179-1186.
   PubMedGoogle Scholar
• VAN ZANTEN-PRZYBYSZ I, MOLTHOFF J, KLEIN-GEBBINCK J et al.: Cellular and humoral responses after multiple injections of unconjugated chimeric monoclonal antibody MOv18 in ovarian cancer patients: a pilot study. J. Cancer Res. Clin. Oncol. (2002) 128(9):484-492.
   PubMed Web of Science ®Google Scholar
• CHOY EH, SCHANTZ A, PITZALIS C, KINGSLEY GH, PANAYI GS: The pharmacokinetics and human anti-mouse antibody response in rheumatoid arthritis patients treated with a chimeric anti-CD4 monoclonal antibody. Br. J. Rheumatol. (1998) 37(7):801-802.
   PubMedGoogle Scholar
• WELT S, RITTER G, WILLIAMS C et al.: Phase I study of anticolon cancer humanised antibody A33. Clin. Cancer Res. (2003) 9(4):1338-1346.
   PubMed Web of Science ®Google Scholar
• SCOTT AM, LEE FT, JONES R et al.: A Phase I trial of humanised monoclonal antibody A33 in patients with colorectal carcinoma: biodistribution, pharmacokinetics, and quantitative tumor uptake. Clin. Cancer Res. (2005) 11(13):4810-4817.
   PubMed Web of Science ®Google Scholar
• RITTER G, COHEN LS, WILLIAMS C, RICHARDS EC, OLD LJ, WELT S: Serological analysis of human anti-human antibody responses in colon cancer patients treated with repeated doses of humanised monoclonal antibody A33. Cancer Res. (2001) 61(18):6851-6859.
   PubMed Web of Science ®Google Scholar
• WELT S, RITTER G, WILLIAMS C et al.: Preliminary report of a Phase I study of combination chemotherapy and humanised A33 antibody immunotherapy in patients with advanced colorectal cancer. Clin. Cancer Res. (2003) 9(4):1347-1353.
   PubMed Web of Science ®Google Scholar
• VINCENTI, LANTZ, BIRNBAUM et al.: A Phase I trial of humanised anti-interleukin 2 receptor antibody in renal transplantation. Transplantation (1997) 63(1):33-38.
   PubMed Web of Science ®Google Scholar
• MENTER A, GORDON K, CAREY W et al.: Efficacy and safety observed during 24 weeks of efalizumab therapy in patients with moderate to severe plaque psoriasis. Arch. Dermatol. (2005) 141(1):31-38.
   PubMed Web of Science ®Google Scholar
• PAPP KA, MILLER B, GORDON KB et al.: Efalizumab retreatment in patients with moderate to severe chronic plaque psoriasis. J. Am. Acad. Dermatol. (2006) 54(4 Suppl. 1):S164-S170.
   PubMed Web of Science ®Google Scholar
• BOECKH M, BERREY MM, BOWDEN RA, CRAWFORD SW, BALSLEY J, COREY L: Phase I evaluation of the respiratory syncytial virus-specific monoclonal antibody palivizumab in recipients of hematopoietic stem cell transplants. J. Infect. Dis. (2001) 184(3):350-354.
   PubMed Web of Science ®Google Scholar
• THE IMPACT-RSV STUDYGROUP: Palivizumab, a humanised respiratory syncytial virus monoclonal antibody, reduces hospitalization from respiratory syncytial virus infection in high-risk infants. Pediatrics (2006) 102(3):531-537.
   Google Scholar
• DJUKANOVIC R, WILSON SJ, KRAFT M et al.: Effects of treatment with anti-immunoglobulin E antibody omalizumab on airway inflammation in allergic asthma. Am. J. Respir. Crit. Care Med. (2005) 170:583-593.
   Web of Science ®Google Scholar
• BUSSE W, CORREN J, LANIER BQ et al.: Omalizumab, anti-IgE recombinant humanised monoclonal antibody, for the treatment of severe allergic asthma. J. Allergy Clin. Immunol. (2001) 108(2):184-190.
   PubMed Web of Science ®Google Scholar
• TOLCHER AW, OCHOA L, HAMMOND LA et al.: Cantuzumab mertansine, a maytansinoid immunoconjugate directed to the CanAg antigen: a Phase I, pharmacokinetic, and biologic correlative study. J. Clin. Oncol. (2003) 21:211-222.
   PubMed Web of Science ®Google Scholar
• WEINBLATT ME, MADDISON PJ, BULPITT KJ et al.: CAMPATH-1H, a humanised monoclonal antibody, in refractory rheumatoid arthritis. An intravenous dose-escalation study. Arthritis Rheum. (1995) 38(11):1589-1594.
   PubMed Web of Science ®Google Scholar
• ISAACS JD, WING MG, GREENWOOD JD, HAZLEMAN BL, HALE G, WALDMANN H: A therapeutic human IgG4 monoclonal antibody that depletes target cells in humans. Clin. Exp. Immunol. (1996) 106(3):427-433.
   PubMed Web of Science ®Google Scholar
• ISAACS JD, WATTS RA, HAZLEMAN BL et al.: Humanised monoclonal antibody therapy for rheumatoid arthritis. Lancet (1992) 340(8822):748-752.
   PubMed Web of Science ®Google Scholar
• ISAACS JD, MANNA VK, RAPSON N et al.: CAMPATH-1H in rheumatoid arthritis-an intravenous dose-ranging study. Br. J. Rheumatol. (1996) 35(3):231-240.
   PubMedGoogle Scholar
• REIFF A: A review of campath in autoimmune disease: biologic therapy in the gray zone between immunosuppression and immunoablation. Hematology (2005) 10(2):79-93.
   PubMed Web of Science ®Google Scholar
• KRAMER, LIEBES, WASSERHEIT et al.: Initial clinical evaluation of radiolabeled MX-DTPA humanised BrE-3 antibody in patients with advanced breast cancer. Clin. Cancer Res. (1998) 4(7):1679-1688.
   PubMed Web of Science ®Google Scholar
• GORDON MS, MARGOLIN K, TALPAZ M et al.: Phase I safety and pharmacokinetic study of recombinant human anti-vascular endothelial growth factor in patients with advanced cancer. J. Clin. Oncol. (2001) 19(3):843-850.
   PubMed Web of Science ®Google Scholar
• MARGOLIN K, GORDON MS, HOLMGREN E et al.: Phase Ib trial of intravenous recombinant humanised monoclonal antibody to vascular endothelial growth factor in combination with chemotherapy in patients with advanced cancer: pharmacologic and long-term safety data. J. Clin. Oncol. (2001) 19(3):851-856.
   PubMed Web of Science ®Google Scholar
• JURCIC JG, DEBLASIO T, DUMONT L, YAO TJ, SCHEINBERG DA: Molecular remission induction with retinoic acid and anti-CD33 monoclonal antibody HuM195 in acute promyelocytic leukemia. Clin. Cancer Res. (2000) 6(2):372-380.
   PubMed Web of Science ®Google Scholar
• GUTHEIL JC, CAMPBELL TN, PIERCE PR et al.: Targeted antiangiogenic therapy for cancer using Vitaxin: a humanised monoclonal antibody to the integrin αvβ3. Clin. Cancer Res. (2000) 6(8):3056-3061.
   PubMed Web of Science ®Google Scholar
• GHOSH S, GOLDIN E, GORDON FH et al.: Natalizumab for active Crohn’s disease. N. Engl. J. Med. (2003) 348(1):24-32.
   PubMed Web of Science ®Google Scholar
• BOWEN JD, PETERSDORF SH, RICHARDS TL et al.: Phase I study of a humanised anti-CD11/CD18 monoclonal antibody in multiple sclerosis. Clin. Pharmacol. Ther. (1998) 64(3):339-346.
   PubMed Web of Science ®Google Scholar
• BORJESSON PKE, POSTEMA EJ, ROOS JC et al.: Phase I therapy Study with 186Re-labeled humanised monoclonal antibody BIWA 4 (bivatuzumab) in patients with head and neck squamous cell carcinoma. Clin. Cancer Res. (2003) 9:3961s-3972s.
   PubMed Web of Science ®Google Scholar
• COLNOT DR, ROOS JC, DE BREE R et al.: Safety, biodistribution, pharmacokinetics, and immunogenicity of 99mTc-labeled humanised monoclonal antibody BIWA 4 (bivatuzumab) in patients with squamous cell carcinoma of the head and neck. Cancer Immunol. Immunother. (2003) 52(9):576-582.
   PubMed Web of Science ®Google Scholar
• CARPENTER PA, APPELBAUM FR, COREY L et al.: A humanised non-FcR-binding anti-CD3 antibody, visilizumab, for treatment of steroid-refractory acute graft-versus-host disease. Blood (2002) 99(8):2712-2719.
   PubMed Web of Science ®Google Scholar
• SANDBORN WJ, FEAGAN BG, HANAUER SB et al.: An engineered human antibody to TNF (CDP571) for active Crohn’s disease: a randomized double-blind placebo-controlled trial. Gastroenterology (2001) 120(6):1330-1338.
   PubMed Web of Science ®Google Scholar
• STEINFELD SD, TANT L, BURMESTER GR et al.: Epratuzumab (humanised anti-CD22 antibody) in primary Sjögren’s syndrome: an open-label Phase I/II study. Arthritis Res. Ther. (2006) 8(4):R129.
   PubMed Web of Science ®Google Scholar
• FEAGAN BG, GREENBERG GR, WILD G et al.: Treatment of ulcerative colitis with a humanised antibody to the α4β7 integrin. N. Engl. J. Med. (2005) 352(24):2499-2507.
   PubMed Web of Science ®Google Scholar
• KOREN E, ZUCKERMAN LA, MIRE-SLUIS AR: Immune responses to therapeutic proteins in humans – clinical significance, assessment and prediction. Curr. Pharm. Biotechnol. (2002) 3:349-360.
   PubMedGoogle Scholar
• CASTELLINO F, ZHONG G, GERMAIN RN: Antigen presentation by MHC class II molecules: invariant chain function, protein trafficking, and the molecular basis of diverse determinant capture. Hum. Immunol. (1997) 54:159-169.
   PubMed Web of Science ®Google Scholar
• DAVIS MM, BJORKMAN PJ: T-cell antigen receptor genes and T-cell recognition. Nature (1988) 334:395-402.
   PubMed Web of Science ®Google Scholar
• STARR TK, JAMESON SC, HOGQUIST KA: Positive and negative selection of T cells. Annu. Rev. Immunol. (2003) 21:139-176.
   PubMed Web of Science ®Google Scholar
• MARSH SG, PARHAM P, BARBER LD: The organisation of HLA genes within the HLA complex. In: The HLA Factsbook. Marsh SG, Parham P, Barber LD (Eds), Academic Press, London, UK (2000):7-13.
   Google Scholar
• GANSBACHER B, ZIER KS: Regulation of HLA-DR, DP, and DQ expression in activated T cells. Cell. Immunol. (1988) 117:22-34.
   PubMed Web of Science ®Google Scholar
• COCHRAN JR, AIVAZIAN D, CAMERON TO, STERN LJ: Receptor clustering and transmembrane signaling in T cells. Trends Biochem. Sci. (2001) 26:304-310.
   PubMed Web of Science ®Google Scholar
• GJERTSON DW, TERASAKI PI: HLA 1998. American Society for Histocompatibility and Immunogenetics, Lenexa, KS, USA (1998).
   Google Scholar
• NO AUTHORS LISTED: Hum. Immunol. (2004) 65:855-1270.
   Web of Science ®Google Scholar
• TSUCHIYA K, KIMURA A, KONDO M, NISHIMURA Y, SASAZUKI T: Combination of HLA-A and HLA class II alleles controls the susceptibility to rheumatoid arthritis. Tissue Antigens (2001) 58:395-401.
   PubMed Web of Science ®Google Scholar
• KONING F: Celiac disease: caught between a rock and a hard place. Gastroenterology (2005) 129:1294-301.
   PubMed Web of Science ®Google Scholar
• LARSEN CE, ALPER CA: The genetics of HLA-associated disease. Curr. Opin. Immunol. (2000) 16:660-667.
   Web of Science ®Google Scholar
• ROH EY, PARK MH, PARK H et al.: Association of HLA-DR and -DQ genes with narcolepsy in Koreans: comparison with two control groups, randomly selected subjects and DRB1*1501-DQB1*0602-positive subjects. Hum. Immunol. (2006) 67(9):749-755.
   PubMed Web of Science ®Google Scholar
• FALK K, ROETZSCHKE O, STEFANOVIC S, JUNG G, RAMMENSEE HG: Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature (1991) 351:290-296.
   PubMed Web of Science ®Google Scholar
• HUNT D, MICHEL H, DICKINSON TA et al.: Peptides presented to the immune system by the murine class II major histocompatibility complex molecule I-A d. Science (1992) 256:1817-1820.
   PubMed Web of Science ®Google Scholar
• RUDENSKY AY, PRESTON-HURLBURT P, HONG SC, BARLOW A, JANEWAY CA Jr: Sequence analysis of peptides bound to MHC class II molecules. Nature (1991) 353:622-627.
   PubMed Web of Science ®Google Scholar
• CHICZ RM, URBAN RG, LANE WS et al.: Predominant naturally processed peptides bound to HLA-DR1 are derived from MHC-related molecules and are heterogeneous in size. Nature (1992) 358:764-768.
   PubMed Web of Science ®Google Scholar
• ENG JK, MCCORMACK AL, YATES JR III: An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. (1994) 5:976-989.
   PubMed Web of Science ®Google Scholar
• DAVENPORT MP, SMITH KJ, BAROUCH D et al.: HLA Class I binding motifs derived from random peptide libraries differ at the COOH terminus from those of eluted peptides. J. Exp. Med. (1997) 185:367-371.
   PubMed Web of Science ®Google Scholar
• OSHITANI N, HATO F, KITAGAWA S et al.: Analysis of intestinal HLA-DR bound peptides and dysregulated immune responses to enteric flora in the pathogenesis of inflammatory bowel disease. Int. J. Mol. Med. (2003) 11:99-104.
   PubMed Web of Science ®Google Scholar
• ROHN TA, REITZ A, PASCHEN A et al.: Novel strategy for the discovery of MHC class II-restricted tumor antigens: identification of a melanotransferrin helper T-cell epitope. Cancer Res. (2005) 65:10068-78.
   PubMed Web of Science ®Google Scholar
• SOUTHWOOD S, SIDNEY J, KONDO A et al.: Several common HLA-DR types share largely overlapping peptide binding repertoires. J. Immunol. (1998) 160:3363-3373.
   PubMed Web of Science ®Google Scholar
• RUDOLF MP, MAN S, MELIEF CJM, SETTE A, KAST WM: Human T-cell responses to HLA-A-restricted high binding affinity peptides of human papillomavirus Type 18 proteins E6 and E7. Clin. Cancer Res. (2001) 7:788s-795s.
   PubMed Web of Science ®Google Scholar
• SIDNEY J, SOUTHWOOD S, OSEROFF C, DEL GUERCIO MF, GREY HM, SETTE A: Measurement of MHC/peptide interactions by gel filtration. In: Current Protocols in Immunology. Wiley, New York, NY, USA (1998):18.13.1-18.13.19.
   Google Scholar
• TANGRI S, MOTHÉ BR, EISENBRAUN J et al.: Rationally engineered therapeutic proteins with reduced immunogenicity. J. Immunol. (2005) 174:3187-3196.
   PubMed Web of Science ®Google Scholar
• DESMET J, MEERSSEMAN G, BOUTONNET N et al.: Anchor profiles of HLA-specific peptides: analysis by a novel affinity scoring method and experimental validation. Proteins (2005) 58:53-69.
   PubMed Web of Science ®Google Scholar
• WARMERDAM PAM, VANDERLICK K, VANDERVOORT P et al.: Staphylokinase-specific cell-mediated immunity in humans. J. Immunol. (2002) 168:155-161.
   PubMed Web of Science ®Google Scholar
• STICKLER M, ROCHANAYON N, RAZO J et al.: An in vitro human cell-based assay to rank the relative immunogenicity of proteins. Toxicol. Sci. (2004) 77:280-289.
   PubMed Web of Science ®Google Scholar
• ANTHONY DD, LEHMANN PV: T-cell epitope mapping using the ELISPOT approach. Methods (2003) 29:260-269.
   PubMed Web of Science ®Google Scholar
• STICKLER M, CHIN R, FARAVASHI N et al.: Human population-based identification of CD4+ T-cell peptide epitope determinants. J. Immunol. Methods (2003) 281:95-108.
   PubMed Web of Science ®Google Scholar
• HARDING F: CD4+ T cell epitope identification: applications to allergy. Clin. Exp. Allergy (2003) 33:557-565.
   PubMed Web of Science ®Google Scholar
• ZHOU LJ, TEDDER TF: CD14+ blood monocytes can differentiate into functionally mature CD83+ dendritic cells. Proc. Natl. Acad. Sci. USA (1996) 93:2588-2592.
   PubMed Web of Science ®Google Scholar
• OSTENSEN M, SICHER P, FORGER F, VILLIGER PM: Activation markers of peripheral blood mononuclear cells in late pregnancy and after delivery: a pilot study. Ann. Rheum. Dis. (2005) 4:318-320.
   Web of Science ®Google Scholar
• SETTE A, BUUS S, APPELLA E et al.: Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis. Proc. Natl. Acad. Sci. USA (1989) 86:3296-3300.
   PubMed Web of Science ®Google Scholar
• MCFARLAND BJ, BEESON C: Binding interactions between peptides and proteins of the class II major histocompatibility complex. Med. Res. Rev. (2002) 22:168-203.
   PubMed Web of Science ®Google Scholar
• PETERS B, TONG W, SIDNEY J, SETTE A, WENG Z: Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. Bioinformatics (2003) 19:1765-1772.
   PubMed Web of Science ®Google Scholar
• 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. J. Exp. Med. (1994) 180:2353-2358.
   PubMed Web of Science ®Google Scholar
• RAMMENSEE H, BACHMANN J, EMMERICH NP, BACHOR OA, STEVANOVIC S: SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics (1999) 50:213-219.
   PubMed Web of Science ®Google Scholar
• STURNIOLO T, BONO E, DING J et al.: Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat. Biotechnol. (1999) 17:555-561.
   PubMed Web of Science ®Google Scholar
• BORRAS-CUESTA F, GOLVANO J, GARCIA-GRANERO M et al.: Specific and general HLA-DR binding motifs: comparison of algorithms. Hum. Immunol. (2000) 61:266-278.
   PubMed Web of Science ®Google Scholar
• SINGH H, RAGHAVA GP: ProPred: prediction of HLA-DR binding sites. Bioinformatics (2001) 17:1236-1237.
   PubMed Web of Science ®Google Scholar
• RECHE PA, GLUTTING JP, ZHANG H, REINHERZ EL: Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles. Immunogenetics (2004) 56:405-419.
   PubMed Web of Science ®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.
   PubMed Web of Science ®Google Scholar
• NIELSEN M, LUNDEGAARD C, WORNING P et al.: Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics (2004) 20:1388-1397.
   PubMed Web of Science ®Google Scholar
• GULUKOTA K, SIDNEY J, SETTE A, DELISI C: Two complementary methods for predicting peptides binding major histocompatibility complex molecules. J. Mol. Biol. (1997) 267:1258-1267.
   PubMed Web of Science ®Google Scholar
• MILIK M, SAUER D, BRUNMARK AP et al.: Application of an artificial neural network to predict specific class I MHC binding peptide sequences. Nat. Biotechnol. (1998) 16:753-756.
   PubMed Web of Science ®Google Scholar
• MAMITSUKA H: Predicting peptides that bind to MHC molecules using supervised learning of hidden Markov Models. Proteins (1998) 33:460-474.
   PubMed Web of Science ®Google Scholar
• ZHAO Y, PINILLA C, VALMORI D, MARTIN R, SIMON R: Application of support vector machines for T-cell epitopes prediction. Bioinformatics (2003) 19:1978-1984.
   PubMed Web of Science ®Google Scholar
• SEGAL MR, CUMMINGS MP, HUBBARD AE: Relating amino acid sequence to phenotype: analysis of peptide-binding data. Biometrics (2001) 57:632-642.
   PubMed Web of Science ®Google Scholar
• DESMET J, SPRIET J, LASTERS I: Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization. Proteins (2002) 48:31-43.
   PubMed Web of Science ®Google Scholar
• DAVIES MN, SANSOM CE, BEAZLEY C, MOSS DS: A novel predictive technique for the MHC class II peptide-binding interaction. Mol. Med. (2003) 9:220-225.
   PubMed Web of Science ®Google Scholar
• DOYTCHINOVA IA, GUAN P, FLOWER DR: Quantitative structure-activity relationships and the prediction of MHC supermotifs. Methods (2004) 34:444-453.
   PubMed Web of Science ®Google Scholar
• BORDNER AJ, ABAGYAN R: Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins (2006) 63:512-526.
   PubMed Web of Science ®Google Scholar
• ANTES I, SIU SW, LENGAUER T: DynaPred: a structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations. Bioinformatics (2006) 22:e16-e24
   PubMed Web of Science ®Google Scholar
• JOJIC N, REYES-GOMEZ M, HECKERMAN D, KADIE C, SCHUELER-FURMAN O: Learning MHC I-peptide binding. Bioinformatics (2006) 22:e227-e235.
   PubMed Web of Science ®Google Scholar
• MARSHALL KW, LIU AF, CANALES J et al.: Role of the polymorphic residues in HLA-DR molecules in allele-specific binding of peptide ligands. J. Immunol. (1994) 152:4946-4957.
   PubMed Web of Science ®Google Scholar
• DOOLAN DL, SOUTHWOOD S, CHESNUT R et al.: HLA-DR-promiscuous T cell epitopes from Plasmodium falciparum pre-erythrocytic-stage antigens restricted by multiple HLA class II alleles. J. Immunol. (2000) 165:1123-1137.
   PubMed Web of Science ®Google Scholar
• NEPOM GT, NEPOM BS: Prediction of susceptibility to rheumatoid arthritis by human leukocyte antigen genotyping. Rheum. Dis. Clin. North Am. (1992) 18:785-792.
   PubMed Web of Science ®Google Scholar