1. Structural Bioinformatics Dr. Avraham Samson Course no.: 81-871 Credit points: 1.5 Final grade is based on 10 assignments Course homepage: http://odem.md.biu.ac.il/sb871

2. 2 Bioinformatics Definition: –“The collection, archiving, organization, and interpretation of biological data.” [Orengo, 2003] Etymology: - Bio- from “biology”, and –informatics from “information science”.

3. Bioinformatics 3 Sequence bioinformatics Structure bioinformatics Systems biology

4. 4

5. 5 Structural Bioinformatics Focus on data sets with molecular structure

6. 6 Structural Bioinformatics Motivation 1: Detailed understanding of molecular interactions

7. 7 Structural Bioinformatics Motivation 2: Lots of structural data is becoming available

8. 8 Outline of today’s lecture Overview of structural bioinformatics –Goals –Challenges –Applications Overview of course –Topics –Lectures –Assignments

9. 9 Structural Bioinformatics Goals: Analysis Visualization Comparison Prediction Design

10. 10 Structural Bioinformatics Goals: Analysis Visualization Comparison Prediction Design

11. 11 Structural Bioinformatics Goals: Analysis Visualization Comparison Prediction Design

12. 12 Structural Bioinformatics Goals: Analysis Visualization Comparison Prediction Design

13. 13 Structural Bioinformatics Goals: Analysis Visualization Comparison Prediction Design

14. 14 Structural Bioinformatics Goals: Analysis Visualization Comparison Prediction Design

15. 15 Structural Bioinformatics Research challenges: Structure prediction Binding site detection Binding site modeling Binding site matching Binding prediction Molecular design etc.

16. 16 Structural Bioinformatics Research challenges: Structure prediction Binding site detection Binding site modeling Binding site matching Binding prediction Molecular design etc.

17. 17 Structural Bioinformatics Research challenges: Structure prediction Binding site detection Binding site modeling Binding site matching Binding prediction Molecular design etc.

18. 18 Structural Bioinformatics Research challenges: Structure prediction Binding site detection Binding site modeling Binding site matching Binding prediction Molecular design etc.

19. 19 Structural Bioinformatics Research challenges: Structure prediction Binding site detection Binding site modeling Binding site matching Binding prediction Molecular design etc.

20. 20 Structural Bioinformatics Research challenges: Structure prediction Binding site detection Binding site modeling Binding site matching Binding prediction Molecular design etc.

21. 21 Structural Bioinformatics Research challenges: Structure prediction Binding site detection Binding site modeling Binding site matching Binding prediction Molecular design etc.

22. 22 Structural Bioinformatics Applications: Biology Medicine Agriculture Industry etc.

23. Overview of course http://odem.md.biu.ac.il/sb871 23

24. 24 y = f(x)  Biologists like experiments, specifics and classifications They like it better to know many (x i,y i ) – i.e., facts – and classify them, than to know f  Computer scientists like simulation, abstractions, and general algorithms They want to know f – the explanation of the facts – and efficient ways to compute it, but rarely care for any (x i,y i )  One challenge of Computational Biology is to fuse these two cultures The Shock of Two Cultures