Day 2: Structural alignment, classification and 1D prediction

Slides

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Exercises

A. Your are studying in the lab the following protein (sequence). Try to obtain as much structural information from the sequence:

  1. Predict its secondary structure with at least two programs (e.g. PSIPRED and Jpred). Compare the results
  2. Are there any structures of close homologs in the PDB?
  3. Compare the secondary structure predicted for your protein to the secondary structure in PDB for the homolog protein
  4. To which family does this homolog protein belong to according to structure classification? (Search SCOP and/or CATH)
  5. Find similar structures in the PDB
  6. Do you find any of those structures in CATH or SCOP databases? How many domains comprise your protein? To which family/superfamily belongs?

B. Analyze these sequences for the identification of probable transmembrane segments, coiled-coils and disordered regions

Resources

Software for structural alignment

Pair-wise and database searches
Multiple structure alignment
Flexible alignments

Protein structure classification

1D prediction

Secondary structure
Transmembrane segments
Transmembrane helices
Transmembrane barrels
Coiled-coils
Disorder
Other 1D prediction tools