http://www.sienabiografix.it/index_edu.php
Protein structure
prediction
Start
End
Uniprot Blast
Clustalo
Modeler
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
Secondary structure prediction
Why predict the secondary structure of proteins?
• 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.
JPRED3
http://www.compbio.dundee.ac.uk/www-jpred/
JPRED3
http://www.compbio.dundee.ac.uk/www-jpred/
Choose file
MAX 800 AA
JPRED3
http://www.compbio.dundee.ac.uk/www-jpred/
JPRED3
JPRED3
JPRED3
JPRED3
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.
Questions!!!!
• From UniProt take Fasta sequence of Bik
Protein Name: Bik ; Organism: Homo sapiens
• Use the tool jpred3 with the query sequence
• Analyze result
Tertiary structure prediction
Homology
Modeling
HHpred
Paste query sequence
HHpred
HHpred
HHpred
HHpred
HHpred
HHpred
Modeller
http://salilab.org/modeller/
HHpred-MSA
1.
2.
Modeller
Modeller
Modeller registration
http://salilab.org/modeller/registration.html
Modeller
Questions!!!!
• Try to build a model for the query sequence, write
all the selected passages.
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.