Tools

Alignment Analysis   Databases   Computational Immunology   Modelling & 3D-structure     Analysis   Sequence Manipulation &     Analysis   Similarity Searches   View all Tools		Tools    >> Rankpep Rankpep: prediction of binding peptides to Class I and Class II MHC molecules Description This server predicts peptide binders to MHCI and MHCII molecules from protein sequence/s or sequence alignments using Position Specific Scoring Matrices (PSSMs). In addition, it predicts those MHCI ligands whose C-terminal end is 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 T cell epitopes [9mer] HLA-A*0101 all [9mer] HLA-A*0201 [8mer] HLA-A*0201 [EPI_OPT] HLA-A*0201 [HIGH BINDERS] 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-E [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-DR15(DRB1*1502) 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 example 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 et al. (2002). Prediction of MHC Class I Binding Peptides Using Profile Motifs. Human Immunology, 63: 701-709. Reche PA et al. (2004) Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles. Immunogenetics, 56:405-419. Reche PA, Reinherz EL (2007) Prediction of peptide-MHC binding using profiles. Methods Mol Biol., 409:185-200. Praises & Complaints: Pedro A. Reche Hits since June/2006 Last updated: Contact Us    |   Immunomedicine Group    |