Table of contents Phyre 2.0 Use General instructions. One to one Instructions. Results

Phyre 2.0

Use

-Phyre 2.0 can be used to create theoretical protein structure based on aligning it's amino acid sequences with the sequence of a protein with a known structure. For best use create a Phyre 2.0 account.
-To create an account simply click on the create account button and enter your information.

General instructions.

-Phyre can preform blast searches to determine what protein would be similar.
-To preform a blast search go to the main page.
-If an email for the results to be sent to isn't present make sure to enter an email address in the 'email address box', results will automatically be sent there.
-Type job name/description in the "optional job description box"
-Paste the amino acid sequence into the box and search. Phyre will automatically generate theoretical structures for each alignment it does. Select the structure most relevant. This process can take take anywhere from 30 minutes to 7 hours.

Figure 1. Phyre 2.0 page used to create theoretical structure using a BLAST search.

One to one Instructions.

If there is a specific protein that is desired to be used a 'one to one' search can be performed.
-Go to expert mode in the top left corner.
-Select 'One to one'
-Type job name/description in the "optional job description box"
-Paste the amino acid sequence of the protein that you wish to generate the theoretical structure for.
-Upload the PDB file of the protein desired as the template.
-Hit submit.
-If the PDB protein has multiple chains select the desired chain.
-Submit. Phyre will take at least 30 minutes to run the alignment and generate the structure.

Figure 2. Phyre 2.0 page used to create theoretical structure based on a selected protein using One to one.

Results

-The results will show the percent identity, confidence, the aligned sequences and aligned structures(Helix, beta sheet), and the theoretical structure can be downloaded as text, FASTA pairwise alignment, or as a 3D model in PDB format.
-Results will be available on Phyre 2.0 for 30 days.

[[Amendola 4 June 2014]]