At the end of a CUMAb run, you will receive two files:
- 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.
- An excel spreadsheet with 3 sheets
- Combinations: This sheet contains instructions on how to combine the light and heavy chain sequences given in the following two sheets.
- Light Chains: This sheet contains the suggested light chain sequences. Each light chain has a “Name”, “Short name”, and “Sequence”. The short name is what is referred to in the combinations sheet.
- Heavy Chains: This sheet contains the suggested heavy chain sequences. Each light chain has a “Name”, “Short name”, and “Sequence”. The short name is what is referred to in the combinations sheet.