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 (FASTA format) End (pdb file) Blast Clustalo Jpred HHpred Modeller Phyre2 Qmean

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. PHYRE2 Protein Fold Recognition Server INSERT SEQUENCE http://www.sbg.bio.ic.ac.uk/~phyre2/html/page.cgi?id=index

5. Phyre2 - Results

7. The prediction is 3-state: either α-helix, β-strand or coil. Green helices represent α-helices, blue arrows indicate β-strands and faint lines indicate coil. The 'SS confidence' line indicates the confidence in the prediction, with red being high confidence and blue low confidence. The 'Disorder' line contains the prediction of disordered regions in your protein and such regions are indicated by question marks (?).

8. Qmean http://swissmodel.expasy.org/qmean/cgi/index.cgi PDB-format

9. Qmean

10. Qmean - Results The estimated residue error is visualised using a colour gradient from blue (more reliable regions) to red (potentially unreliable regions, estimated error above 3.5 Å).

11. Qmean - Results Large negative values correspond to red regions in the color gradient. "Good structures" are expected to have all sliders in the light red to blue region.

12. Questions 1.Qmean score per una proteina in banca dati 2.Qmean score per un aproteina modellata (Hhpred)

13. Domain Structural Motifs Structural Domains Aminoacid GLY = Glicin 1° 2° 3°4° (helix-turn-helix)

14. InterPro http://www.ebi.ac.uk/interpro/

15. InterPro - Results

16. GENE ONTOLOGY The Gene Ontology project provides controlled vocabularies of defined terms representing gene product properties.

17. Polymerization http://en.wikipedia.org/wiki/RNA-dependent_RNA_polymerase

18. https://www.ebi.ac.uk/thornton-srv/databases/enzymes/

19. Capping 5’ http://en.wikipedia.org/wiki/MRNA_(guanine-N7-)-methyltransferase

21. http://www.dnatube.com/video/1220/The-RNAdependent-RNA-polymerase