Georg Casari's models
Procedure
Ls,
In this area you will find two models. The first model was made
by Georg Casari in 1989, using the alignment that is given in the
article. The second model was made using an alternative alignment
that Georg and I came up with in 1997...
The old model was refined and energy minimised (in vacuum, using GROMOS).
We used WHAT IF to
automatically build the second model.
If you are interested, you can get some
information about
the methods used to build the second model.
Remarks
With the percentage identity as present in this case, it is not possible to build
models with any reliability, unless there is a considerable body of experimental
knowledge available. This was the case, and teh original model built (not given here)
was only constructed (with 1989 state of the art software...) to indicate that the
detected homology would not be incompatible with a 3D structure.
There is, however, no need saying that we have not yet found the correct alignment.
Many residues are not put in the model at all, and those that are there are not always
modelled equally well. However, the active site seems perfect, and several other aspects
of the model agree really well with experimental data.
So, although from a technical point of view both models are shitty, they are good enough
to suggest experiments, and even good enough to answer a few biologically relevant questions.
Models
view or get the first model
view or get another model
Quality
Before looking at the model quality, please keep in mind that:
- We maintain as much as possible the template backbone in the model. Even in case
of mutations from or to Gly or Pro. This sometimes leads to big local errors, but avoids
many global errors.
- The backbone quality normally gets worse upon modelling. The techniques to do this better simply
do not yet exist.
- We do not try to remove all small clashes. This sometimes leads to local errors, but avoids
many global errors.
- Judging by the numbers only, the models look rather shitty. It simply cannot be done
much better with the given sequence identity to the template.
- B-factors of modelled atoms are set at 12.0. So the B-factor validation is useless.
- Other Xray tests are useless too (e.g. Mattwevs volume, cell dimensions...).
The reports:
GV, Last modified Aug 24, 1997