Tutorial

Note: Throughout this tutorial you can click on the images to enlarge them.

1. Submit the loop to be modelled by FREAD

A
Select the pdb file with missing loops or with loops you want to model. If the file actually contains a loop the RMSD of the modelled loop with the one in the file is displayed in the results page. For this tutorial you may use this file. Note that the pdb file should only contain a single chain. Click on Select PDB File and select the pdb file (e.g. 1JGZM.pdb). You should see a progress bar while the file is uploading.
B
Once the file is uploaded enter 257 as the residue number. This is the position of the first residue number of the loop. Note that the loop end will be computed by using this position and the length of the sequence entered in the next step.
C
Enter the amino acid sequence of the loop, GFNATMEG. If these residues are defined in the pdb file, these must match the entered sequence otherwise an error message will be shown.
D
Select the database to use for the loop modelling. Note that the larger the database, the more time the modelling will take. Select All Proteins.
E
This score will determine what kind of substitutions will be allowed in the residue sequence entered in Step C (use a lower score for a perfect match). The default is 25. For the purpose of this tutorial, do not enter anything in this field.
F
Sets the RMSD difference allowed at the anchor residues (the beginning and end of the loop). The default value is 1.0Å. For the purpose of this tutorial, do not enter anything in this field.
G
When you are ready from the above steps press this button to submit the FREAD job (doh!).

2. Please Wait...

Once your modelling job is submitted, you should see this "Please Wait" page. The time taken to process your job depends on the number of other jobs in the queue. This may take a few minutes. This page will automatically refresh and take you to the results page when ready. Alternatively, if you need to close the internet browser you can bookmark the URL and return to it for your results at a later stage.

3. Results

The results page is presented as shown on the left.

A
Click on this link to get a detailed explanation of every column in the results table
B
You can download all the results (in a zip file). This bundle will include the whole protein with the modelled loop as well as the modelled loop fragment in a separate file.
C
If you are only interested in a particular model, you can click on the fragment name to download it as a pdb file.
D
The last column of the results table initially displays a Show option. When this link is clicked the model is displayed in a Java Applet (JMol) and the option to hide it is made available to the user (this replaces the original Show option).
E
The model may be interacted with using the mouse (rotation, zoom, translation). The modelled loop is shown in a different colour (red) than the rest of the model (grey).