Tutorial

General

SuperLooper is a user friendly tool for the modelling of loops, with an emphasis on the modelling of membrane protein loops. SuperLooper can be used intuitively, but info buttons guide you throughout the whole modelling process.

Start

In order to model a loop, you first have to upload a protein structure. Click the item SuperLooper on in the main menu on the left, then please provide your protein model or crystal structure in PDB file format. Press "submit" to start the application.

Input

After pressing the "submit" button, your structure will be uploaded into the protein viewer. If you have uploaded a membrane protein (e.g. B2-adrenergic G protein-coupled receptor, 2RH1) the membrane planes will be displayed in the viewer, as soon as the calculation has finished. The planes may be shown or hidden by the according buttons.

Enter the number of the amino acid that precedes the gap in the protein and of the amino acid that succeeds the gap to be filled in. Select the chain identifier using the selectbox. (This information maybe taken from the text icon that appears when the mouse pointer is positioned over the stem amino acids in the protein viewer.)

Now please type or paste the amino acid sequence (in one letter code) of the desired loop into the input field "sequence". The sequence must not be longer than 35 residues.

Click the "loop search" button to initiate the search for loop candidates.

Inspect loop candidates

The database search is completed within a few seconds and the results are ranked in the table right to the visualisation window, with loops taken from LIMP being ranked first. Proper loops may be chosen by visual inspection (after selection of the according radio button) of the candidates in the viewer, the alignment information provided in a box below the viewer and by the consideration of the following guidelines:

• High scores (see: Interactive Search, SuperLooper, 3.) indicate good loop candidates
• The less the RMSD_stem, the better the loop
• RMSD_stem < 0.3 Å
• minimal distance > 2.4 Å
• if possible, maximal distance < cutoff,
  where cutoff = 4.5 * ln(loop length) + 4 (as a rule of thumb, see LIP paper [3])
• For membrane proteins, please check the position of the loop relative to the membrane planes
• Avoid loop amino acid sequences with false prolines* or glycines** in order to avoid incorrect backbone torsion angles

Finishing

As soon as you have found the appropriate loop, please click the button "accept loop".
You now have the opportunity to add further loops to your protein or to download your structure, using the respective buttons.

Screenshots