How do I use the Project Mode mode of SWISS-MODEL
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 (Swiss-PdbViewer
Guex et al).The user has therfor 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.)
- Get the template in the correct quaternary
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, PQS will most likely have the correctly
assembled coordinate file for you. In our example: [PQS
entry for 3HVP].
Download and save the template coordinates as PDB file to your local disk
- 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).
- 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.
- 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]
Adjust target-template Alignment in DeepView
- Load the FASTA file into DeepView (Menu: Swissmodel),
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.
- 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.
[ Modelling ] [ Project
Model of the dimeric protease.