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.php

Start(FASTA format)

End (pdb file)

Blast Clustalo Jpred HHpred Modeller

Phyre2Qmean

Protein structure prediction

1. Modeling by homology2. Ab initio

3. Fold Recognition

Protein Sequence Experimental Data

MSA Research in databases Assigning domains

Secondary structure prediction Prediction Fold

Homology modelingTertiary 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

PHYRE2 Protein Fold Recognition Server

INSERT SEQUENCE

http://www.sbg.bio.ic.ac.uk/~phyre2/html/page.cgi?id=index

Phyre2 - Results

Phyre2 - Results

Phyre2 - Results

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 (?).

Qmean

http://swissmodel.expasy.org/qmean/cgi/index.cgi

PDB-format

Qmean

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).

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.

Questions

1. Qmean score per una proteina in banca dati2. Qmean score per un aproteina modellata

(Hhpred)

Domain

Structural Motifs

Structural Domains

AminoacidGLY = Glicin

1° 2° 3° 4°

(helix-turn-helix)

InterPro

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

InterPro - Results

InterPro - Results

GENE ONTOLOGY

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

Polymerization

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

Polymerization

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

Capping 5’

http://en.wikipedia.org/wiki/MRNA_(guanine-N7-)-methyltransferase

Capping 5’

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