Protein structure prediction
29/01/2015
Mail: Prof. Neri Niccolai [email protected] Simone Gardini [email protected]
http://www.sienabiografix.it/index_edu.php
Start(FASTA format)
End (pdb file)
Blast Clustalo Jpred HHpred Modeller
Phyre2Qmean
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
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 - 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)
InterPro - Results
GENE ONTOLOGY
The Gene Ontology project provides controlled vocabularies of defined terms representing gene product properties.