CUMAb Results

At the end of a CUMAb run, you will receive four files:

1) A pymol session containing the variable regions of the Fv of the originally uploaded PDB (and the antigen if given), as well as the suggested designs.

• In the pymol session, the Fv of the originally uploaded pdb is shown in cyan, and the antigen, if given, is shown in green. The suggested Fv designs are shown in white, with mutations from the original Fv shown in sticks and colored according to the difference in the BLOSUM90 matrix between the original residue and the designed one. The color is on a spectrum from blue to red, where blue is very similar and red is very dissimilar.

2) An excel spreadsheet with 3 sheets

• The first sheet ("Combinations") contains the five suggested humanized combinations of light and heavy chains. The remaining two sheets ("Light and Heavy Chains"), contain the amino acid sequences of the humanized designs for the light and heavy chains, respectively. In each of these two sheets, each humanized light or heavy chain has a "Name," which is the IMGT germline on which the design is based. Additionally, each sequence has a "Short name", which is what the "Combinations" sheet refers to. Finally, there is the humanized amino acid sequence.

3) A csv containing the Rosetta scores of every sequence modeled in CUMAb.

4) A csv containing the cluster representatives after CUMAb clustering and their Rosetta scores.

If the excel spreadsheet (item 2) is empty, this means that CUMAb could not find any humanized sequences that have a calculated energy comparable to that of the inputted antibody. If this happens, please feel free to reach out to us and we will look in more detail at the specific case.