Structural bioinformatics

General information

This lecture course, accompanied by a practical exersise, is being offered in winter semester. It is suitable for bioinformatics students of the 5th semester and higher.

 

Recommended reading

  • Structural bioinformatics (Methods of biochemical analysis, v.44). Bourne, P. and Weissig, H., editors. Wiley-Liss, 2003.
  • Lesk, A.. Introduction to Protein Architecture: The Structural Biology of Proteins. Oxford University Press, 2001.
  • Branden, C.I. & Tooze, J. Introduction to Protein Structure: Second Edition. Routledge, 1999.
  • Zvelebil, M. and Baum, J. Introduction to bioinformatics. Garland Science, 2007.
  • Mount, D. Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor Laboratory Press; 2 edition, 2004.

 

List of topics

  • Introduction to structural bioinformatics
  • Protein structure
  • Molecular visualization
  • Secondary structure assignment
  • Structure determination
  • Structure quality
  • Structural databases
  • Structure comparison
  • Identification of structural domains
  • Structure classification
  • Protein structures: an overview
  • Protein folding
  • Docking
  • Homology modeling
  • Secondary structure prediction
  • Transmembrane region prediction
  • Coiled coils
  • Low complexity, non-globular, and disordered regions
  • Signal peptides
  • Contact prediction
  • Threading
  • CASP
  • Genomes and folds
  • Target selection
  • Extreme environment
  • Protein-protein interactions
  • Protein evolution
  • Structure-function relationships in proteins
  • Functionally important residues
  • Local sequence motifs
  • Exons and domains
  • Alternative splicing and protein structure
  • Mutations and their effect on structures
  • Structure design