- Protein Structure Modeling 117
- Homology modeling with SwissModel
You may choose SwissModel, ModWeb, or I-tasser, or all of them to
do homology modeling. Difference between SwissModel and I-tasser are
described in ‘I-tasser’ section.
Materials
- Accession number of your protein in UniProt database, or sequence of your
protein of interest. To get accession number of a protein, please check the
previous section.
Procedure
I. Navigate to UniProt (http://www.uniprot.org/), or search UniProt in
the search engine (If you possess your protein sequence, please skip to
step VI. If you wish to give up the opportunity of downloading and
saving protein sequence while you have its accession number, you may
proceedtostepVItoo.)
II. Input accession number into the search bar and hit ‘search’.
III. Check the information shown on the page to ensure that the informa-
tion on that page is about your protein before you proceed.
IV. Navigate to ‘Sequence section by clicking ‘Section’ button on the left
panel.
V. Click on the ‘FASTA’ button above the box displaying your sequence
and copy the FASTA sequence shown. If there are multiple isoforms,
please check all of them and pick one matching your need. It is
recommended to save the sequence along with the model created by
SwissModel to your hard drive together (Fig. 3(a)).
VI. Navigate to SwissModel (http://swissmodel.expasy.org/) or search it
in the search engine. Hit ‘start modeling’ button on the welcome page
(Fig. 3(b)).
VII. Paste the protein sequence or UniProt accession number into ‘Target
Sequence’ field. Fill others accordingly. For other acceptable input
format, please refer to the right panel of this screen. It is highly
recommended that you fill ‘email’ field so that the result will be mailed
to you inbox after the modeling is completed.
If something goes wrong while you input target sequence, press ‘Reset
Form’ button and do it again.