http://www.sienabiografix.it/index_edu.php
Protein structure
prediction
Start
End
(FASTA format)
(pdb file)
Blast Clustalo Jpred
HHpred Modeller
Phyre2
Qmean
Mail:
29/01/2015
Prof. Neri Niccolai neri.niccolai@unisi.it
Simone Gardini simone_gardini@hotmail.com
Protein structure prediction
1.
Modeling by homology
2. Ab initio
3. Fold Recognition
Flowchart
modeling of
proteins
Protein Sequence
Experimental Data
MSA
Research in databases
Assigning domains
Homologous
protein in the
PDB
database?
Secondary structure
prediction
NO
YES
Analysis of the
family fold
Alignment of
secondary structures
Homology modeling
3D Model of Protein
Prediction Fold
Alignment sequence
to structure.
YES
Was
predicted
a fold?
NO
Tertiary structure
prediction
PHYRE2 Protein Fold Recognition Server
http://www.sbg.bio.ic.ac.uk/~phyre2/html/page.cgi?id=index
INSERT SEQUENCE
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
PDB-format
http://swissmodel.expasy.org/qmean/cgi/index.cgi
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 dati
2. Qmean score per un aproteina modellata
(Hhpred)
Domain
Aminoacid
GLY = Glicin
1°
2°
3°
Structural Motifs
(helix-turn-helix)
Structural Domains
4°
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