To generate a 2D plot for a given protein descriptor, firstly you should provide a list of PDB chains to be structurally aligned. To select a chain belonging to a publicly available structure, inform the PDB entry code and click Add (Figure 1A). A list containing all the available chains for the given PDB entry will be shown for selection (Figure 1B). To select a chain just click the respective register. All the selected chains for the structural alignment procedure will be listed just bellow the input form (Figure 1C).
MSSP also accepts STING TGZ files (generated by STING server for user-modeled protein structures). To add a TGZ file, use the Browse button to select your local file and the click Add (Figure 2A). When uploading is finished, all the available chains within the TGZ file will be listed for selection (Figure 2B).
Finally, verify if the selected chains are correct, select the structural alignment program (MUSTANG or MAMMOTH-mult) and then click the respective launch button (green button located just above the Selected PDB chains panel).
Alternatively the user can use option Launch Demo on the main menu to launch MSSP for three predefined cases, which are as follow:
Specifically for the JavaScript version, the user can also choose between two visualization programs (Fig. 3): JSmol (JavaScript Jmol) and Protein Viewer (PV). Protein Viewer is the default option.
Due to renderization constraints, PV will only work properly with structural alignments generated by MUSTANG (MAMMOTH-mult creates structural alignments containing only Cα coordinates. PV cannot properly render protein structures based on such sparse information about the main chain atoms).