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  1. Identify the source of your sequence and the location of the fragment represented by this sequence in the protein.
  2. If the source protein is not annotated, find a similar annotated protein to infer the biological significance of your fragment.
  3. Check if the three-dimensional structure of your fragment is known.
  4. Predict secondary structure for the selected sequence.
  5. Predict three-dimensional structure for the selected sequence using homology modeling.
  6. Analyze the quality of your model using one of the structure assessment tools.
  7. Provide structural classification for your model.
  8. Create a visualization of your model highlighting and annotating one of the important molecular or biological features.
  9. Compare predicted secondary structure with the secondary structure in 3D model and interpret the results.
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