Example of output is found below. The output is divided into the folowinng sections:
- Query sequence:
In this section the query sequence that you submitted are shown in fasta format.
- Searching for template:
The template for building the model is sought by iteratively building up a
profile by aligning the query sequence to a nonredundant database of protein
sequences and then searching a database of proteins with known structure (pdb)
to find a suitable template for making a model.
- Retrieving template:
In this section the pdb entry name and the chain identifier are listed for the
template that are used to construct the model.
- Making profile-profile alignment:
In this section the score fro the profile profile alignment (in bits) and the
percentage sequence identity between query and template are shown together
with the alignment in "Blast-like" format.
By clicking on the link "model.pdb" you can download the coordinates in
pdb format to your own computer.
- PDB3D: If you have an java enabled browser the C-alpha trace of the model
will be shown. You can rotate it by klicking on it with the left mouse button
and holding it down while mooving the mouse. The right mouse button can be used to scale the