Pross examples

Example 1

Task: stabilize an enzyme (pdb code 4XAD)
The enzyme is a monomer (chain A) and was crystallized with a substrate analogue (identifier is 3ZW). The scientist will not specify the chloride ions (CL) as ligands since they seem to be part of the crystallization salt and are not involved in function. She also knows from previous data that ASN44 and LEU56 are important for function.

Query parameters
Email address: <my_email>@<academic domain> <-- email must be from an academic domain and may include up to three digits.
Do you wish to upload your own PDB file? no
PDB id: 4XAD
Chain identifier to design: A
Small-molecule ligands: 3ZW
Interacting chains: leave empty
Specific residues to fix: 44A 56A
Do you wish to upload your own Multiple Sequence Alignment? no
*Use default parameters for the multiple sequence alignment generation unless you have a good reason to change them.

How to handle the results?
Before ordering genes read carefully the readme file (will be attached in the final email) and the results section in the about page.

Example 2

Task: stabilize the human growth hormone (pdb code 1HWG)
PyMOL inspection shows that chain A is the hormone and it interacts with chains B and C. The scientist also read a paper stating that a helical kink between positions 91-97 is important for function.

Query parameters
Email address: <my_email>@<academic domain> <-- email must be from an academic domain and may include up to three digits.
Do you wish to upload your own PDB file? no
PDB id: 1HWG
Chain identifier to design: A
Small-molecule ligands: leave empty
Interacting chains: B C
Specific residues to fix: 91A 92A 93A 94A 95A 96A 97A
Do you wish to upload your own Multiple Sequence Alignment? no
*Use default parameters for the multiple sequence alignment generation unless you have a good reason to change them.

How to handle the results?
Before ordering genes read carefully the README file (will be attached in the final email) and the results section in the about page.