1. Protein structure prediction 29/01/2015 Mail: Prof. Neri Niccolai neri.niccolai@unisi.it Simone Gardini simone_gardini@hotmail.com http://www.sienabiografix.it/index_edu.phpStart End Uniprot Blast ClustaloModeler

2. Protein structure prediction 1.Modeling by homology 2.Ab initio 3.Fold Recognition

3. Protein SequenceExperimental Data MSA Research in databases Assigning domains Secondary structure prediction Prediction Fold Homology modeling Tertiary structure prediction Alignment sequence to structure. Alignment of secondary structures Analysis of the family fold Homologous protein in the PDB database? Was predicted a fold? 3D Model of Protein YES YES NO NO Flowchart modeling of proteins

4. Secondary structure prediction To study the relationship between structure and function. To study the molecular phylogeny. To determine the relationship between proteins with low sequence similarity. For the design of new proteins and mutants. For the prediction of the tertiary structure. To choose the best alignment for the Homology Modeling. Why predict the secondary structure of proteins?

5. JPRED3 http://www.compbio.dundee.ac.uk/www-jpred/

6. http://www.compbio.dundee.ac.uk/www-jpred/ MAX 800 AA Choose file

7. JPRED3 http://www.compbio.dundee.ac.uk/www-jpred/

11. What are do the characters 'E', 'H', 'B' and '-' represent in the prediction? They represent extended (E), helical (H) and other (-) types of secondary structure respectively. In the solvent accessibility predictions they represent buried (B) and exposed (-) for each of the 0%, 5% and 25% solvent accessibility cut-offs.

12. Questions!!!! From UniProt take Fasta sequence of Bik Protein Name: Bik ; Organism: Homo sapiens Use the tool jpred3 with the query sequence Analyze result

13. Tertiary structure predictionHomologyModeling

14. HHpred Paste query sequence

15. HHpred

21. Modeller HHpred-MSA 1. 2. http://salilab.org/modeller/

22. Modeller

24. Modeller registrationhttp://salilab.org/modeller/registration.html

25. Modeller

26. Questions!!!! Try to build a model for the query sequence, write all the selected passages.

27. Questions!! Use jpred3, hhpred and modeler to build a model for rna pol ebola. Remember that the sequence is very long, so you'll have to split the sequence. When you have finished writing the report. Good job.