From Human Salivary Proteome Wiki
Structure Prediction
The structure of a protein gives rise to its functions. Even though a large number of proteins already have their structures determined experimentally, e.g. through X-ray crystallography, there are still many proteins whose structures remain unresolved. Therefore, many computational methods have been developed to predict the structure of a protein using only its amino acid sequence.
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Phyre2
Phyre2 is one of the most popular homology-based methods for protein structure prediction. It builds a profile of the input sequence and matches this profile with similar profiles in a large database of proteins with known 3D structures. Since the structure of a protein is typically more conserved than its sequence, even a distantly related protein can provide hints on the structure of the protein in question. However, the accuracy of the predicted structures is not guaranteed.
Using the Protein Structure Prediction special page
The form on the Special:PredictStructure page is an interface to the remote Phyre2 server. Note that this analysis can take a few hours to more than a day to complete. In addition to the protein sequence, the email field is required because you will be notified by email when the job is finished.
On a protein page
Click on the Tools tab on the right of the page, and follow the "3D Structure Prediction" link on the menu. It will take you to the Protein Structure Prediction form with all the fields pre-populated. If the protein has multiple sequence variants, the canonical sequence will be used by default.
See also: Help:Salivary Proteins
Display of Results
After a job has submitted, a message will appear with a link to the status page of the job on the Phyre2 server. You can monitor the status on that page or wait for the email automatically sent after the job is completed. Attached in the email is the top predicted model in PDB format and the associated confidence level in that model. The result page on the Phyre2 website will in addition show other possible models and other more detailed information (Fig. 1). The prediction results are typically kept online for 30 days.
References
Kelley LA, et al. (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10(6):845-58. doi:10.1038/nprot.2015.053 [PubMed:25950237]
