Usage

Data Input

Users can upload and analyze new protein structures by clicking on the "Submit new job" button under the "My jobs" menu. Initially, the user must upload a CIF file containing the structure. Upon successful upload, the protein structure is visualized using the Mols* viewer, and a list of chains within the protein is displayed (Figure 1). Subsequently, users have various options to choose according to what he/she would like to analyze the given protein.

• If the user wishes to analyze only specific chains rather than the entire structure, they can remove unwanted chains by clicking on the chain name in the list. To select multiple chains, hold Shift and click; to deselect, use Ctrl+click. Removed chains will appear in gray in the structure (Figure 2).



Figure 2



If the user wishes to analyze only specific chains rather than the entire structure, they can remove unwanted chains by clicking on the chain name in the list.
• Since the determination of membrane regions can be hindered by the presence of antibodies used during protein crystallization and/or structure determination (e.g., antibodies in 8tb7 are located within the membrane region), users can automatically remove these by clicking the "Unselect antibodies" button (Figure 3).
• Some transmembrane proteins curve the membrane during their function (e.g., the mechanosensitive ion channel). The new TmDet algorithm allows for the detection of curved membrane surfaces. Users can enable this feature by clicking the "Search For Curved Membrane" button.
• If a user wants to examine a protein model that was generated without considering the structural constraints imposed by the lipid bilayer, the modeling program may fold globular parts of the protein into the membrane region, alongside the transmembrane regions. This is a common error in AlphaFold modelled transmembrane protein structures. To detect such errors, users can select the "Fragment Analysis" option.



Figure 3



Since the determination of membrane regions can be hindered by the presence of antibodies used during protein crystallization and/or structure determination (e.g., antibodies in 8tb7 are located within the membrane region), users can automatically remove these by clicking the "Unselect antibodies" button

Please note that both the curved membrane and fragment analyses take significantly longer time to complete than the simple planar membrane detection, and may last several minutes depending on the protein size and server load.

Job List

After a successful submission, or by selecting the "My jobs" menu, user can view a list of their submitted jobs and their status (Processing or Completed). For completed jobs, user are able to investigate the results, share the job by copying its url, or delete the job.

Results viewer

On this page, users can analyze/handle the results in 5 panels.

• Summary tab:
  This tab displays some basic information such as the protein code, protein type (Tm_Alpha, Tm_Beta, TM_Mixed, or Soluble for non-transmembrane proteins), and the resulting qValue (more information about this is available on the Description page).



Figure 3



3D tab displays the protein embedded in the membrane using the Mol* molecule viewer. The lipid bilayer is represented by gray spheres, and the individual regions are colored according to their position relative to the membrane (the meaning of the colors is explained on the bottom of the page)
• 1D tab:
  This tab shows the amino acid sequences of each protein chain in fasta format, colored according to the region types (color codes are provided on the bottom of the page). The viewer uses the auth_asym_id specified in the cif file to identify the protein chains.
• 3D tab:
  Clicking the view button opens the 3D tab, which displays the protein embedded in the membrane using the Mol* molecule viewer. The lipid bilayer is represented by gray spheres, and the individual regions are colored according to their position relative to the membrane (the meaning of the colors is found on the Legend tab). Hovering the mouse over an element of the structure, Mol* displays the region type and the starting and ending residue numbers (Figure 4).
• Download tab:
  On this tab, you can download both an XML file containing the annotated types of the regions and a cif file containing the transformed structure and the atoms representing the membrane region, as well as view them in their raw form. Additionally, users can download these files as a zipped archive.