1. The Protein Data Bank. The PDB format. Using the RCSB PDB web interface.
2. Structure validation.
Precision and accuracy.. Sources of errors in NMR and X-ray structures. The Ramachandran map. Molecular features usable for validation.
3. Assignment of secondary structure elements.
definition of secondary structure elements. Identification of hydrogen bonds. Overview of several assignment algorithms (DSSP, STRIDE, DEFINE, STICK).
4. Structure classification and hierarchical databases I.
Scope of structure classification. The CATH and SCOP databases. The PDB SELECT collection.
5. Structure classification and hierarchical databases II.
Using classification methods in bioinformatical problems.
6. Structure comparison, algorithms and applications I.
Hardness and general description of the comparison problem.
7. Structure comparison, algorithms and applications II.
Overview of several structure comparison methods (DALI, CE, SSAP, GRATH, VAST, PRIDE).
8. Identification of structural domains in proteins.
Domain definitions and their problems.Pronciples of first and second generation algorithms (DOMAK, DETECTIVE, PUU, STRUDL, DomainParser).
9. Structure-function assignments I.
Evolutionary relationships, structural and sequential similarity. Levels of protein function.
10. Structure-function assignments II.
Databases with functional assignments. Prediction of function from structure.
11. Identification of functionally important residues in proteins.
The correlated mutation analysis.
12. Residue networks in proteins.
Contact order, long-range order and their uses. Protein structures as networks. Identification of stabilizing interactions and residues in proteins.
13. Structure of nucleic acids.
Structural variability of base pairs. Structure stabilizing interactions in nucleic acids. Catalytic nucleic acids. Prediction of RNA secondary structure.
14. Introduction to protein structure prediction.
The CASPs and their importance. Classification of prediction tasks. Predictions in 1D (secondary structure, transmembrane helices etc.) Prediction applications on the WWW.
Textbook: P.E. Bourne és H. Weissig (eds.): Structural Bioinformatics. Wiley-Liss, 2003.
Online course material: http://www.chem.elte.hu/departments/protnmr/szerkbioinf/