Modeling sACE2 and decoy receptors

Go to Norimatsu Lab Google drive>Lab projects folder>COVID-19 Project folder>Modeller folder>Templates folder>Mac/Linux or Windows folder (choose whatever system your computer is)>download the template

Open File Explorer. Go to Downloads folder.

Find the template folder. Open and then Extract all.

In the Extracted template folder open the folder work.

Within the work folder, open the model ALI file. You may have to open with Notepad or another program.

Model ALI file contains two primary sequences the top should say >P1; In, and the bottom should say >P1; Out. Each sequence starts at the 21st amino acid, but the amino acid numbers in the sequence are twenty behind. When you place your cursor at the beginning of the sequence it should say 21 but it says 1.

Now go to Norimatsu Lab website, open Lab Projects, COVID-19 project, current progress (link at the bottom of the page), find the correct mutations for the template.

Open the Model ALI file (keeping step 6 in mind) make the mutations in the file and save the changes.

Open Command Prompt and open the extracted template file. Copy and paste the local address of your file explorer to your command prompt it should look something like cd C:/Users/yourusername/Downloads/work.

Once, you have the directory to your template folder opened run mod9.25 and model.py. You should get the message “import site” failed; use -v for traceback. Modeller won’t say when it’s done, so go and check the folder and files should be generating.

Once modeller is done running open each PDB file generated and look for the lowest DOPE score (greatest absolute value).

Upload the file with the lowest DOPE score to google drive. Lab Project> COVID-19 Project> Decoys.