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 input PDB (and the antigen if given), as well as the suggested designs. The pymol session also includes ABodyBuilder2 models of the input sequence and the 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 BLOSUM90 difference 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) A CSV with the light and heavy Fv sequences for the input antibody and the designs

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