Completionist Model Completion for Membrane, Soluble and Ig-like Proteins

Help

 

Before you begin

 

System Requirements

  • A browser that supports frames, JavaScript and Java. The author recommends Mozilla Firefox.
  • Sun Java or compatible.

Input Data Format

Your input should be a membrane protein sequence and a structure. Make sure your input is in the correct format.

  • Input sequences must be provided as pure amino acid sequences, without titles or comments (e.g. "ACDEFG").
  • Input structures must be in PDB format.

Step by step

 

Submitting your query

  1. Go to the box entitled "Complete target sequence". Copy and paste your data into a text area. Make sure your input contains only the amino acid letters (e.g. "ACDEFG") and no titles or comments.
  2. Go to the box entitled "Incomplete model structure". Pick a way to provide your input. You can either upload a file or copy and paste your data into a text area. Make sure that any data you provide here is in PDB format.
  3. Go to the box entitled "Options". Choose the type of protein you are modelling. This can be either a soluble or membrane protein, or an immunoglobulin-like protein (e.g. an antibody). This choice will determine which fragment database will be used for the FREAD loop modelling step. Any loops not modellable with FREAD will be filled using the MODELLER ab initio method.
  4. The last box: "Submit". Press the "Submit" button once, and only once please, to submit your query. Your browser may stay inert from a few seconds up to several minutes (in some cases), while it uploads your input to our web site. If you are unsure whether you have successfully clicked the button, have a look at your browser's status bar. If this starts with something like "Sending", "Waiting" or "Uploading" then everything is fine and you simply need to wait. The screen should automatically refresh and forward you to your results.

Viewing your results

The results screen consists of 2 main frames:

  • Left: The model structure viewer.
  • Right: This area lists all your generated models and some links where you can view or download these.
The structure viewer

This frame shows three-dimensional representations of your models. The structure is coloured by modelling confidence, i.e. the model core has high confidence (coloured blue) whereas loop coordinates have lower confidence and ab-initio loops have the lowest conficence (coloured red).
You can turn the molecule by clicking and dragging it with the left mouse button. Right-clicking gives various view options. Consult the Jmol manual for details.

The results list

The text at the top of the Results list mentions your result's Result ID. Make a note of this or bookmark the link to your result page to come back to it later. Note, however, that your result will only be saved for about 24 hours before being deleted from the server.

The list of models shows several models of increasing coverage: core (your input), hiacc (high accuracy model, with high accuracy database loops), hicov (high coverage model, with high and low accuracy database loops) and complete (the complete model with high and low accuracy database loops and all remaining gaps filled with ab initio methods). The complete model is the only model containing sidechains, terminal residues not present in the input model as well as very long gap regions (>30 residues). These are all co-ordinates that are very hard to model and are usually inaccurate. We do not attempt to model them and leave it to MODELLER to provide placeholder co-ordinates, for your convenience only. The complete model is shown by default.

If you are interested in high-accuracy sidechains, we suggest you try specialised sidechain modelling sofware, such as SCWRL.