Example

In this example, we will construct structure models for the 59 residue fragment of an uncharacterized protein form horse (F6VMN7). We will run 10 threading algorithms, eThread and finally, we will build three-dimensional models using Modeller as well as TASSER-Lite.

Note: Larger output files generated in this tutorial are gzipped.

First, download the amino acid sequence for F6VMN7 from the Uniprot website: http://www.uniprot.org. The downloaded file should be saved in plain FASTA format as : F6VMN7.fasta. Place it in some directory, in this example we will do the modeling in the example/ directory. Edit the input file so it looks exactly like this:

F6VMN7.fasta

>F6VMN7 59
VPPAFCLEPPYVGRCRAMIRRYFYNATSAQCETFTYGGCRQKKNNFISKEECLKTCRGE

This tutorial is divided into three sections: threading, structure modeling and the detailed description of the output files.

 

© Michal Brylinski
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