In the following example, we will create a diversified library of light and heavy chain interfaces of antibody (pdb code 2FJG. This antibody was crystallized in a complex and we choose to model the variants on chain H (heavy) and L (light) of the antibody.
In this step you will enter the parameters of your protein to be modeled, so we could calculate the possible sequence space (i.e., the allowed amino acid identities in each interface position). Make sure you choose the correct pair of light and heavy chains!!
Email address: email@example.com
Do you wish to upload your own PDB file? no
PDB ID: 2FJG
Chain identifier to design: L,H,W
Amino acid positions to diversify: 43L,49L,55L,89L,94L,95L,97L,100L,59H,95H,107H
Use default parameters for the multiple sequence alignment generation.
After setting the parameters for the first step, we calculate the possible sequence space in the light heavy chain interfaces. It may take a few hours/ days.
When the first step is done, you will receive an email with a link to select the parameters for the second step (below).
The parameters set in this step will restrict the exhaustive modeling of all possible multipoint mutants.
Important: be patiant when clicking verify. Some calculations are long and sometimes the page loads very slowly. We are working to faster solutions.
Minimal number of mutations per design: 4 (all mutants are different from the WT protein by at least 4 mutations in the light heavy chain interfaces)
Maximal number of mutations per design: 10 (all mutants are different from the WT protein by at most 10 mutations in the light heavy chain interfaces)
Minimal PSSM threshold: -1 (this chosen threshold value -1, is a bit permissive, in case you want the sequence space to include only amino acids that are favored by the multiple sequence alignment choose a value above or equal to 0)
ΔΔG: 1 (reduce this parameter if the total number of designs is high)
Change the values of the different parameters and click verify to check whether this parameters combination is acceptable (at least 500 mutants, and not more than 500,000).
When satisfied with the resulted sequence space, press the proceed button to proceed to a screen where you will be able to edit manually(add and/ or remove) the sequence space. For example, you could eliminate combinations that could result in deamidation
A few hours/ days after you submit the second step parameters you will get an email with the results. Please read carefully the attached ReadMe.txt file
See the FAQ for furthur details.