Bioinformatics - WHAT IF servers

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2 Οκτ 2013 (πριν από 3 χρόνια και 10 μήνες)

75 εμφανίσεις

©CMBI 2002

Homology modelling ?



X
-
ray ?

NMR ?

Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Homology Modelling !



Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Helices are Helices



Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Strands are Strands



Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Structure=Conservation



Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Structure=Conservation



Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Modelling beats X
-
ray



Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Data ~ infinite…



Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

Copied from TIBS special volume on bioinformatics

©CMBI 2002

What can be Modelled ?



Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

What can be Modelled ?



Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

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


Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Template detection

Normally BLAST is good
enough.


If BLAST doesn’t find a
template, you should not want
to build a model anyway.


When desperate, use PSI
-
BLAST (on PDB + SwissProt),
or use threading.

Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Threading

Threading means using
information from the
template structure to:



detect homology


to improve an alignment.

Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Threading

Small residues

Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Threading

Alcoholic residues

Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Threading

The folded ‘protein’

Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Threading

Two aligned ‘proteins’

Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Alignment

BLAST the model sequence.

BLAST the template sequence.

Select 50
-
100 representatives.

Do multiple sequence
alignment.

Keep only model and template
from that multiple sequence
alignment.


Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

How to align:

ASASASASASAS


YPYPYPYPYPYP


(three ways…)

Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

How to align:

ASASASASASAS
-

AYAYAYAYAYAY
-

-
YPYPYPYPYPYP


(two ways…)

Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Alignment optimization

1 Use threading techniques.

2 Shift gaps around (indels):

Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Select ‘best’ template



Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Deal with errors



Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Exchange side chains



Keep template rigid.

Determine best rotamer.

Do NOT optimize rotamers.

If best rotamer doesn’t fit,
start thinking.

If the model is bad, you had the
wrong template, or the wrong
alignment.

Make sure your model can
exist.


Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Position specific rotamers



Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Position specific rotamers



Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Position specific rotamers



Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

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.


Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Model Optimization



Do NOT use molecular dynamics
(unless you know that you know
what you are doing):


Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Model Optimization



Use 25


50 steps energy
minimization, or use a force
field that has been
especially designed for the
optimization of homology
models.


Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

Validation



Use the WHAT_CHECK server.
(Next seminar).

Use your brains.

Compare with structures.

Compare with Meta
-
server.


Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate

©CMBI 2002

The ‘8’ Steps of Modelling



Depending on the
WHAT_CHECK result, you can
restart at each of the previous
steps in the modelling process.


Intro

Proteins

Modelling

8 Steps

Detect

Threading

Alignment

Template

Side chain

Indels

Optimize

Validate

Iterate