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How do I use the Project Mode mode of SWISS-MODEL workspace ?

Main application: Visual inspection of alignments; modelling of Oligomeric proteins.

In difficult modeling situations, where the correct alignment between target and template cannot be clearly determined by sequence based methods, visual inspection and manual manipulation of the alignment can significantly help improving the quality of the resulting model. Project files containing the superposed template structures, and the alignment between the target and the template can be generated using the program DeepView. The user has therefore full control over essential modelling parameters, i.e. the choice of template structures, the correct alignment of residues, and the placement of insertions and deletions in the context of the three-dimensional structure.
Modelling of oligomeric proteins with Swiss-Model Workspace can be done using the Project Mode.

The program DeepView can be downloaded freely from the ExPASy web site. DeepView does not require administrator privileges for installation. E.g. under MS windows, simply uncompress the distributed archive at any location you like (e.g. c:\spdbv or on your desktop) and start working by starting the spdbv.exe application. Tutorials, manuals and discussion group for DeepView can be found on the DeepView web site.

Example: Modelling a dimeric protein

In order to demonstrate Oligomer-Modelling, we are goint to build a model of the protease of murine leukemia virus based on the PDB file 3HVP. (Please keep in mind that this just an example to illustrate the workflow, presumably there would be much better templates available.)

  1. Get the template in the correct quaternary state
    First, check the correct biological assembly of your template protein. Copies of the assymetric unit of the PDB files can be generated by applying the correct crystallographic symmetry operators. If you are unsure how to do this, PISA will most likely have the correctly assembled coordinate file for you. In our example: [PISA entry for 3HVP].
    Download and save the template coordinates as PDB file to your local disk [3hvp_dimer.pdb].
  2. Remove all non-aminoacid residues
    Open the file in DeepView and remove all non-aminoacid groups such as ions, ligands, OXT, etc. from the template (unless they are at the very end of the file). You can do this by selecting the groups in the control panel of DeepView and Remove the selected residues ("Build" menu).
  3. Ensure Unique Chain IDs
    Make sure each chain has a unique name, e.g. "A","B", etc. Coloring the molecule by chain helps to check.
  4. Target Sequence
    In our example, we will model the protease domain of murine leukemia virus (UniProt AC: P03356). As you can see, the virus encoded pol polyprotein consists of several domains. Before modelling, it make things easier to focus on the interesting segment. You may use e.g. the IprScan utility to identify the individual domains. In our case, we will use residue 3-100.

    Create a FASTA file with your target sequences for each chain in the SAME order as in the template, i.e. "A", then "B" etc separated by semicolons. [target.txt]


  5. Adjust target-template Alignment in DeepView
    - Load the FASTA file into DeepView (Menu: Swissmodel),
    - generate a preliminary target-template alignment (Menu: Fit - Fit raw sequence)
    - open the alignment window and adjust alignment. Make sure NOT to align residues of different chains. Do not align to "non aminoacid residues" like het groups, OXT. Make sure all insertions & deletions are correctly positioned in the structural context.

  6. SWISS-MODEL Submission
    Save the project to your local disk [e.g. dimer_project.pdb] and submit the file to the project mode of SWISS-MODEL workspace for model building. A new workunit will be created, containing the modelling results, includung log file, ANOLEA evaluation, and model project file of the modelled dimer.

Model of the dimeric protease.