Example 1

Task: Humanize an antibody with an appropriate solved structure without the antigen

In this case, w e have a pdb file called Ab1.pdb, in which there is the structure of the antibody of interest. The chain identifiers are unimportant, but there should be one chain for the light chain and one chain for the heavy chain.

Query parameters:

Email address: youremail@academic_institute.edu

Submission name: Anything that you choose

Structure: Upload Ab1.pdb

Antigen Chain: None

Number of designs: 5

Example 2

Task: Humanize an antibody with an appropriate solved structure with the antigen

In this case, we have a pdb file called Ab2.pdb, in which there is the structure of the antibody of interest as well as the antigen. The chain identifiers are unimportant, but there should be one chain for the light chain, one chain for the heavy chain, and one chain for the antigen. In this case, the identifier for the antigen is C.

Query parameters:

Email address: youremail@academic_institute.edu

Submission name: Anything that you choose

Structure: Upload Ab2.pdb

Antigen Chain: C

Number of designs: 5

Mode: CDR

Example 3

Task: Humanize an antibody with an appropriate solved structure with the antigen using SDR-grafting

In this case, we have a pdb file called Ab3.pdb, in which there is the structure of the antibody of interest as well as the antigen. The chain identifiers are unimportant, but there should be one chain for the light chain, one chain for the heavy chain, and one chain for the antigen. In this case, the identifier for the antigen is C.

Note: SDR grafting was tested only on one anti-lysozyme antibody and thus we do not recommend it as a first pass. However, you are welcome to try it J

Query parameters:

Email address: youremail@academic_institute.edu

Submission name: Anything that you choose

Structure: Upload a pdb file of your antibody

Antigen Chain: C

Number of designs: 5

Mode: SDR