Homology modelling

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Homology modelling ?
NMR ?

X-ray ?
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Homology Modelling !

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Helices are Helices

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Strands are Strands

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StructureConservation

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StructureConservation

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Modelling beats X-ray

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Data infinite

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What can be Modelled ?

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What can be Modelled ?

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The 8 Steps of Modelling
1 Detect template 2 Get alignment 3 Optimize
alignment 4 Optimize template 5 Exchange side
chains 6 Deal with insertions/deletions 7
Optimize model 8 Validate 9 Iterate

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The 8 Steps of Modelling
1 Detect template 2 Get alignment 3 Optimize
alignment 4 Optimize template 5 Exchange side
chains 6 Deal with insertions/deletions 7
Optimize model 8 Validate 9 Iterate

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Template detection
Normally BLAST is good enough. If BLAST doesnt
find a template, You should not want to build a
model. When desperate, use PSI-BLAST (on PDB
SwissProt), or use threading.
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Threading
Threading means Use information from the
template structure to detect homology, or to
improve an alignment.
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Threading
Small residues
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Threading
Alcoholic residues
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Threading
The folded protein
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Threading
Two aligned proteins
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The 8 Steps of Modelling
1 Detect template 2 Get alignment 3 Optimize
alignment 4 Optimize template 5 Exchange side
chains 6 Deal with insertions/deletions 7
Optimize model 8 Validate 9 Iterate

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Alignment
Run BLAST on model sequence Run BLAST on template
sequence Select 50-100 representatives Do
multiple sequence alignment Keep only model and
template
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How to align
ASASASASASAS YPYPYPYPYPYP (three ways)
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How to align
ASASASASASAS- AYAYAYAYAYAY- -YPYPYPYPYPYP (two
ways)
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The 8 Steps of Modelling
1 Detect template 2 Get alignment 3 Optimize
alignment 4 Optimize template 5 Exchange side
chains 6 Deal with insertions/deletions 7
Optimize model 8 Validate 9 Iterate

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Alignment optimization
1 Use threading techniques. 2 Shift gaps around
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The 8 Steps of Modelling
1 Detect template 2 Get alignment 3 Optimize
alignment 4 Optimize template 5 Exchange side
chains 6 Deal with insertions/deletions 7
Optimize model 8 Validate 9 Iterate

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Select best template

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Deal with errors

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The 8 Steps of Modelling
1 Detect template 2 Get alignment 3 Optimize
alignment 4 Optimize template 5 Exchange side
chains 6 Deal with insertions/deletions 7
Optimize model 8 Validate 9 Iterate

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Exchange side chains
Keep template rigid Determine best rotamer Do NOT
optimize rotamers If best rotamer doesnt fit,
start thinking. If the model is bad, you had the
wrong template, or the wrong alignment. Make sure
your model exists

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Position specific rotamers

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Position specific rotamers

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Position specific rotamers

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The 8 Steps of Modelling
1 Detect template 2 Get alignment 3 Optimize
alignment 4 Optimize template 5 Exchange side
chains 6 Deal with insertions/deletions 7
Optimize model 8 Validate 9 Iterate

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Insertions - Deletions
Insertions are impossible Deletions Move gap
around in template till end point distance is
short. If this is not possible, you have either
the wrong template, or the wrong alignment.

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The 8 Steps of Modelling
1 Detect template 2 Get alignment 3 Optimize
alignment 4 Optimize template 5 Exchange side
chains 6 Deal with insertions/deletions 7
Optimize model 8 Validate 9 Iterate

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Model Optimization
Do NOT use molecular dynamics

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Model Optimization

Use 25 50 steps energy minimization, or use a
force field that has been especially designed for
the optimization of homology models.
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The 8 Steps of Modelling
1 Detect template 2 Get alignment 3 Optimize
alignment 4 Optimize template 5 Exchange side
chains 6 Deal with insertions/deletions 7
Optimize model 8 Validate 9 Iterate

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The 8 Steps of Modelling
1 Detect template 2 Get alignment 3 Optimize
alignment 4 Optimize template 5 Exchange side
chains 6 Deal with insertions/deletions 7
Optimize model 8 Validate 9 Iterate