Tools     Tools Home   Immunology   Sequence Searches   Sequence Manipulation   Structure Analysis   DNA & Protein Analysis   View all Tools    Tools    >> Rankpep: Prediction of peptide binding to MHC molecules Description This server predicts MHCI- and MHCII-peptide binders from protein sequence or sequence alignments using Position Specific Scoring Matrices (PSSMs). In addition, it predicts those MHCI ligands whith a C-terminal end is that likely to be the result of proteasomal cleavage. A detailed explanation of the method can be found here. PSSM SELECT PSSM (Check MHCI or MHCII) MHC I MHC II H2-Db (mouse) [8mer] H2-Db (mouse) [9mer] H2-Db (mouse) [10mer] H2-Db (mouse) [11mer] H2-Dd (mouse) [9mer] H2-Dd (mouse) [10mer] H2-Dd (mouse) [11mer] H2-Kb (mouse) [8mer] H2-Kb (mouse) [9mer] H2-Kd (mouse) [8mer] H2-Kd (mouse) [9mer] H2-Kd (mouse) [10mer] H2-Kd (mouse) [11mer] H2-Kk (mouse) [8mer] H2-Kk (mouse) [9mer] H2-Ld (mouse) [9mer] H2-M3 (mouse) [10mer] H2-Qa-2a (mouse) [9mer] H2-d (mouse) [10mer] H2-k (mouse) [10mer] HLA-A*0101 [9mer] HLA-A*0201 [8mer] HLA-A*0201 [9mer] HLA-A*0201 [10mer] HLA-A*0201 [11mer] HLA-A*0202 [9mer] HLA-A*0203 [9mer] HLA-A*0204 [9mer] HLA-A*0205 [9mer] HLA-A*0206 [9mer] HLA-A*0207 [9mer] HLA-A*0209 [9mer] HLA-A*0214 [9mer] HLA-A*0301 [9mer] HLA-A*0301 [10mer] HLA-A*0301 [11mer] HLA-A*01 [9mer] HLA-A*01 [10mer] HLA-A*11 [9mer] HLA-A*11 [10mer] HLA-A*11 [11mer] HLA-A*1101 [9mer] HLA-A*1101 [10mer] HLA-A*02 [9mer] HLA-A*02 [10mer] HLA-A*02 [11mer] HLA-A*24 [8mer] HLA-A*24 [9mer] HLA-A*24 [10mer] HLA-A*2402 [9mer] HLA-A*2402 [10mer] HLA-A*2402 [11mer] HLA-A*2902 [9mer] HLA-A*03 [9mer] HLA-A*03 [10mer] HLA-A*03 [11mer] HLA-A*31 [9mer] HLA-A*31 [10mer] HLA-A*3101 [9mer] HLA-A*3101 [10mer] HLA-A*3301 [9mer] HLA-A*3301 [10mer] HLA-A*6601 [9mer] HLA-A*68 [10mer] HLA-A*6801 [9mer] HLA-A*6801 [10mer] HLA-A*6801 [11mer] HLA-A*6802 [9mer] HLA-B*0702 [9mer] HLA-B*14 [9mer] HLA-B*15 [9mer] HLA-B*1501(B62) [9mer] HLA-B*1501(B62) [10mer] HLA-B*1502 [9mer] HLA-B*1508 [9mer] HLA-B*1509 [9mer] HLA-B*1510 [9mer] HLA-B*1513 [9mer] HLA-B*1516 [9mer] HLA-B*1517 [9mer] HLA-B*18 [9mer] HLA-B*27 [9mer] HLA-B*27 [10mer] HLA-B*2701 [9mer] HLA-B*2702 [9mer] HLA-B*2703 [9mer] HLA-B*2704 [9mer] HLA-B*2705 [8mer] HLA-B*2705 [9mer] HLA-B*2705 [10mer] HLA-B*2706 [9mer] HLA-B*2709 [9mer] HLA-B*35 [8mer] HLA-B*35 [9mer] HLA-B*3501 [8mer] HLA-B*3501 [9mer] HLA-B*3501 [10mer] HLA-B*3501 [11mer] HLA-B*3801 [9mer] HLA-B*39011 [9mer] HLA-B*39011 [8mer] HLA-B*3909 [9mer] HLA-B*4002 [9mer] HLA-B*44 [9mer] HLA-B*44 [10mer] HLA-B*4402 [9mer] HLA-B*4403 [9mer] HLA-B*4403 [10mer] HLA-B*51 [9mer] HLA-B*51 [10mer] HLA-B*5101 [9mer] HLA-B*5102 [9mer] HLA-B*5103 [9mer] HLA-B*53 [9mer] HLA-B*5301 [9mer] HLA-B*5301 [10mer] HLA-B*5401 [9mer] HLA-B*5502 [9mer] HLA-B*5701 [9mer] HLA-B*5702 [9mer] HLA-B*5801 [9mer] HLA-B*61 [9mer] HLA-B*62 [9mer] HLA-B*07 [9mer] HLA-B*07 [10mer] HLA-B*07 [11mer] HLA-B*08 [8mer] HLA-B*08 [9mer] HLA-B*08 [10mer] HLA-B*08 [11mer] HLA-Cw*0102 [9mer] HLA-Cw*0304 [9mer] HLA-Cw*0702 [9mer] HLA-G [9mer] HLA-x [9mer] HLA-DP4 HLA-DP9(DPA1*0201xDPB1*0901) HLA-DPw4 HLA-DPw4(DPB1*0402) HLA-DQ1 HLA-DQ1(DQA1*0101xDQB1*0501) HLA-DQ2(DQA1*0501xDQB1*0201) HLA-DQ2(DQA1*0501xDQB1*02) HLA-DQ5(DQA1*0101xDQB1*0501) HLA-DQ6(DQA1*0102xDQB1*0602) HLA-DQ7 HLA-DQ7(DQB1*0301) HLA-DQ8(DQA1*0301xDQB1*0302) HLA-DR1 HLA-DR11(DRB1*1101) HLA-DR11(DRB1*1104) HLA-DR11(DRB3*1101) HLA-DR11(DRB3*1102) HLA-DR11(DRB3*1103) HLA-DR11(DRB3*1104) HLA-DR12(DRB1*1201) HLA-DR13(DRB1*1301) HLA-DR13(DRB1*1302) HLA-DR14 HLA-DR15(DRB1*1501) HLA-DR17 HLA-DR17(DRB1*0301) HLA-DR1(DRB1*0101) HLA-DR1(DRB1*0102) HLA-DR2 HLA-DR3 HLA-DR4 HLA-DR4(DRB1*0401) HLA-DR4(DRB1*0402) HLA-DR4(DRB1*0404) HLA-DR4(DRB1*0405) HLA-DR4(DRB1*0406) HLA-DR4(DRB1*0407) HLA-DR5 HLA-DR51(DRB5*0101) HLA-DR52(DRB3*02) HLA-DR53 HLA-DR53(DRB4*0101) HLA-DR6 HLA-DR7 HLA-DR7(DRB1*0701) HLA-DR8(DRB1*0801) HLA-DR9 HLA-DR9(DRB1*0901) I-Ab I-Ad I-Ag7 I-Ak I-Ap I-Aq I-As I-Au I-Eb I-Ed I-Ek I-Es OR, UPLOAD YOUR PSSM INPUT TYPE: FASTA sequence/s CLUSTALW multiple sequence alignment Replace sample with your query >A56881 PIR2 release 71.00 MWNLLHETDSAVATARRPRWLCAGALVLAGGFFLLGFLFGWFIKSSNEAT NITPKHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQW KEFGLDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPG YENVSDIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKI VIARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPG GGVQRGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYY DAQKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTN EVTRIYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVR SFGTLKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYI NADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKK SPSPEFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNKFSGYP LYHSVYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDY AVVLRKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERL QDFDKSNPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKY AGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA OR, UPLOAD SEQUENCES BINDING THRESHOLD PERCENTAGE: 2 % 3 % 4 % 5 % 6 % 7 % 8 % 9 % 10 % 15 % 20 % TOP NUMBER: 5 10 15 20 30 990 PROTEASOME CLEAVAGE FILTER: OFF ON LMPC : One Two Three If Filter is ON only peptides predicted to be cleaved are shown ADVANCED OPTONS RESTRICT RESULTS BY MW Lower Limit for Molecular Weight Upper Limit for Molecular Weight VARIABILITY MASKING Select Variability Threshold Value must range between 0.0 and 4.3 Citation: Reche PA, Glutting JP and Reinherz EL. Prediction of MHC Class I Binding Peptides Using Profile Motifs. Human Immunology 63, 701 709 (2002). Questions, and suggestions to: Pedro Reche Mirror Site at: Immunomedicine Group, Facultad de Medicina, Universidad Complutense de Madrid, SPAIN. Hits since June/2002 Last updated: MIF Bioinformatics    |   Molecular Immunology Foundation    |