ZIBAffinity User Manual

ZIBAffinity is an easy-to-apply software that can be used to compute the binding affinity of small ligand molecules to given protein structures. After you have purchased ZIBAffinity on the market place, after you have uploaded your protein and ligand structures in the data calatogue, and after you have initiated your HPC- or cloud infrastructure, you can run the simulations. For these steps we refer to the MSO4SC-portal documentation. For the preparation of ligands and proteins according to the GROMACS standards you can visit the tutorial page:

1. Login and Instance creation

First we need to login to the MSO4SC portal, we can do it at portal.mso4sc.eu site, after successful login we can navigate to the Experiments menu.

login screen

Figure 1: Login screen of the MSO4SC portal.

After login we see the MSO4SC dashboard

frontend

Figure 2: The MSO4SC dashboard.

Now follow these steps:

  1. For this choose „Instances / Add new one“

  2. Select ZIBAffinity from the pull-down-list (some more inputs occur)

  3. Chose an arbitrary DeploymentID (e.g.42)

  4. Press „Create Instance“

  5. Select your list of ligands from the pull-down-list „Data ressource: lig“ (saved in the data catalogue)

  6. Select your protein structure from the pull-down-list „Data ressource: tar“ (saved in the data catalogue)

  7. Chose the HPC primary (which is the HPC-instance that you have initiated before)

  8. Add a "0" (indicated as a string) in the za_charge field. If your ligand is charged, then change this number according to the positive or negative (integer) value

  9. Add your eMail-Adress for getting the results of the simulation (mandatory!)

  10. Click „Create Instance“ and wait.

  11. Chose your Instance (Deployment ID) from the pull-down-list.

  12. Click run.

Now the simulations will be perfomred and the results will be send to your indicated email. In the eMail you will find the estimated binding affinity value in kJ/mol plus a ziped-directory of attached pdb-files which contains the estimated protein-ligand-complexes. These files can be visualized using VMD (e.g.) For a better understanding oft he procedure watch our tutorial video: youtu.be/kVK6hpIYTGs