{"id":814,"date":"2021-06-30T13:57:24","date_gmt":"2021-06-30T12:57:24","guid":{"rendered":"https:\/\/pbwww.services.came.sbg.ac.at\/?page_id=814"},"modified":"2021-06-30T14:07:24","modified_gmt":"2021-06-30T13:07:24","slug":"mhcii3dweb-help","status":"publish","type":"page","link":"https:\/\/pbwww.services.came.sbg.ac.at\/?page_id=814","title":{"rendered":"MHCII3dweb Help"},"content":{"rendered":"

MHCII3D is a tool for predicting MHC-II binding peptides, based on structural scaffolds of MHC-II-peptide complexes and statistical scoring functions (SSFs).<\/p>\n

MHCII3D provides two modes:<\/p>\n

    \n
  1. the scoring of peptides, and<\/li>\n
  2. the scan of a protein sequence for binding regions<\/li>\n<\/ol>\n

    Scoring a list of peptides<\/h2>\n

    For all prediction modes, first a HLA-DRB allele needs to be selected.<\/p>\n

    Then\u00a0 a list of peptides needs to be entered, either on peptide per line or in multi-fasta format.<\/p>\n

    \"\"<\/a><\/p>\n

    Output<\/h4>\n

    \"\"<\/a><\/p>\n\n\n\n\n\n\n\n\n\n
    Column<\/th>\nMeaning<\/th>\n<\/tr>\n
    Allele<\/td>\nBeta chain allele name<\/td>\n<\/tr>\n
    Peptide<\/td>\nInput sequence<\/td>\n<\/tr>\n
    Binding Sequence<\/td>\nBinding Sequence in the 15-mer peptide scaffold. ‘-‘ characters indicate that the peptide is shorter than the scaffold or shifted to the left or to the right. For clarity, the 9-mer core is indicated here in magenta.<\/td>\n<\/tr>\n
    Binding Score<\/td>\nSSF based score, the more negative the better<\/td>\n<\/tr>\n
    Binding Rank<\/td>\nnormalized rank of the score in a random background ranging from zero (optimal) to one (worse than lowest scoring random peptide).<\/td>\n<\/tr>\n
    IC50<\/sub> predicted<\/td>\nRank converted to a IC50<\/sub> value by non-linear fit<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

    Scan a protein sequence for binding regions<\/h2>\n

    Here, only a single sequence may be given, either as plain sequence or in fasta format. The input sequence is cut into overlapping fragments and each fragment is subsequently scored.<\/p>\n

    \"\"<\/a><\/p>\n

    The meaning of the respective columns is described in the table above.<\/p>\n

    In addition, three plots are given, showing the average of the binding score, rank and IC50<\/sub> per residue. Watch out for minima in these plots in order to locate binding regions (potential T-cell epitopes).<\/p>\n","protected":false},"excerpt":{"rendered":"

    MHCII3D is a tool for predicting MHC-II binding peptides, based on structural scaffolds of MHC-II-peptide complexes and statistical scoring functions (SSFs). MHCII3D provides two modes: the scoring of peptides, and the scan of a protein sequence for binding regions Scoring a list of peptides For all prediction modes, first a HLA-DRB allele needs to be … Continue reading MHCII3dweb Help<\/span> →<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-templates\/full-width.php","meta":[],"_links":{"self":[{"href":"https:\/\/pbwww.services.came.sbg.ac.at\/index.php?rest_route=\/wp\/v2\/pages\/814"}],"collection":[{"href":"https:\/\/pbwww.services.came.sbg.ac.at\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/pbwww.services.came.sbg.ac.at\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/pbwww.services.came.sbg.ac.at\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/pbwww.services.came.sbg.ac.at\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=814"}],"version-history":[{"count":10,"href":"https:\/\/pbwww.services.came.sbg.ac.at\/index.php?rest_route=\/wp\/v2\/pages\/814\/revisions"}],"predecessor-version":[{"id":827,"href":"https:\/\/pbwww.services.came.sbg.ac.at\/index.php?rest_route=\/wp\/v2\/pages\/814\/revisions\/827"}],"wp:attachment":[{"href":"https:\/\/pbwww.services.came.sbg.ac.at\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=814"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}