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Protein Preparation Requirements

The recommended protein preprocessing should include:

  1. Removal of unnecessary cofactors, solvents, etc.

  2. Removal of unnecessary protein chains.

  3. Reconstruction of missing atoms/residues.

  4. Selection of positions in case of multiple alternative conformations.

  5. Addition of disulfide bridges.

  6. Assignment of partial charges, protonation.

  7. Geometry optimization through energy minimization (with or without a solvent).

Creating a project​

To create a project:

  1. Press the “Add Project” button on your main dashboard.

  2. Enter the project name, select a prepared protein file in .pdb format, and add an optional description.

  3. If the uploaded .pdb file passes necessary checks, the “Confirm” button will become active. Press “Confirm” to create your project.

Handling cofactors​

When cofactors are detected in the uploaded file, a pop-up will appear asking whether you want to keep small molecules, water, and ions.

Options:​

  • Option “Yes”: Allows you to select one of the detected small molecules as a reference ligand. This molecule will be excluded from calculations performed by the models but will serve as a reference for binding site analysis.

    • After selecting “Yes”, a list of detected small molecules will appear in the sidebar.

    • Choose the desired molecule by clicking the circle next to it and press “Confirm” to finalize.

    • This menu also allows you to remove the small molecule from the PDB file.

  • Option “No”: Retains all detected small molecules as cofactors in the protein file and includes them in subsequent calculations.

Options:​

  • Option “No”: Removes all small molecules, water, and ions from the protein file, ensuring a cleaner preparation for further analysis.
  • Option “Yes”: Retains small molecules, water, and ions in the file. You will then be prompted to decide if any of the detected small molecules should be used as a reference ligand.

If you press “Yes” and a small molecule is detected in the protein file, a second pop-up menu will appear, asking how you want to handle the detected ligand.