Homology modelling ? X-ray ? NMR ?. Homology Modelling !

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Text of Homology modelling ? X-ray ? NMR ?. Homology Modelling !

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  • Homology modelling ? X-ray ? NMR ?
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  • Homology Modelling !
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  • Helices are Helices
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  • Strands are Strands
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  • Structure=Conservation
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  • Structure=Conservation
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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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  • 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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  • 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