FCCC    Clusters of Antibody CDR Loop Conformations     Dunbrack Lab


A user can submit either an antibody structure in the PDB format or sequences in fasta format to have it renumbered, and its CDRs identified. For a PDB structure, the clusters are also identified.

  • Structure

    A user can submit a PDB structure containing antibody from the local machine. The file must have .pdb as its extension name, and must be in the PDB format. The CDRs of the sequences in the input structure are predicted from our antibody HMM models and HMMER3.0. CDRs are assigned to CDR HMMs based on E-value. The E-value cutoff is 1E-5. Then structure is processed, clusters are identified.

    Submit a PDB

    Figure1: PDB submit page.

    In figure 2, the first table shows the domains and genes, and the HMMER scores and E-values. The second table gives the CDRs, clusters and the new numbers. In upper right, a download button is to download a text file and the renumbered structure file. The text file contains the details about CDRs and clusters.

    Result for a PDB submit

    Figure 2: The CDRs and clusters of the input PDB structure.

  • Sequences

    Submit sequences either by pasting in the text box or upload a file. The file must be in .fasta as extension and the sequences must be in the fasta format. The sequences are assigned to CDRs HMM models by HMMER3.0.

    Submit Sequences

    Figure 3: Sequences submit page.

    The result page for sequences input shows two tables: the first table shows the chains, domains and HMMER scores and E-values. The second table lists the CDRs and the new numbers. The output file can be downloaded by the Download button.

    Result for Sequences Submit

    Figure 4: The CDRs of the input sequences