Hi there, I got one hunderd models. The side-chain torsion angles of the interesting residues are vary. Does anybody know why. Does MODELLER calculate the torsion based on some rules or it is by chance.
Cheers
BinBin
On Wed, Mar 24, 2004 at 11:56:16AM +0000, Binbin Liu wrote: > I got one hunderd models. The side-chain torsion angles of the interesting > residues are vary. Does anybody know why. Does MODELLER calculate the torsion > based on some rules or it is by chance.
The torsion angles are determined by the restraints acting on the corresponding atoms. These are in turn taken from the defined dihedral angles in the topology and parameter files - e.g. modlib/top_heav.lib and modlib/par.lib. See also http://salilab.org/modeller/FAQ.html#17
The angles are different in the different models because the starting conditions for each model are different, and there are many local minima in this sort of optimization problem.
Ben Webb, Modeller Caretaker
On Wed, 24 Mar 2004 11:56:16 +0000 Binbin Liu bmbbl@bmb.leeds.ac.uk wrote:
> Does anybody know why. Does MODELLER calculate the torsion > based on some rules or it is by chance.
Modeller calculates each structure by an algorithm that uses random numbers to search for the best positions for each part of the molecule. This means that each structure will differ slightly, even though the same data (the templates) were used as input to the algorithm. This is why you see the variation - its not really by chance though. There are energy functions involved in side-chain placement, and a final optimisation stage that moves them around so they don't touch too much.
Side chain torsion angles are actually quite difficult to get right - they are the 'fine detail' of structure, and making them perfect means having a highly accurate model of the system. There are tools dedicated to modelling side-chains efficiently - search for SCWRL by Roland Dunbrack at the fox chase CRC, for one example. Even then, if the model of the backbone is not perfect, then the side-chains are not likely to be 100% correct.
j. _______________________________________________________________________ Dr JB Procter:Biomolecular Modelling at ZBH - Center for Bioinformatics Hamburg http://www.zbh.uni-hamburg.de/staff.php
Liu,
Your problem deals essentially with side chains. You have to know that all programs of homology modeling have difficulties for prediction of side chains and results are often bad... Basically, at the biginning, programs choose conformation of side chains of templates in conditon that the same residuse are aligned. If it is not the case, the side chain is placed and is minimized. So, it is logical whether your side chains are different between your models because the minimization depends on the local environnement.
I hope you have understood what i had tried to explain...
With regards, Mickaël
On Wed, 24 Mar 2004, Binbin Liu wrote:
> Hi there, > I got one hunderd models. The side-chain torsion angles of the interesting > residues are vary. Does anybody know why. Does MODELLER calculate the torsion > based on some rules or it is by chance. > > > Cheers > > > BinBin > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage >
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Binbin Liu -
J B Procter -
Mickael Krzeminski -
Modeller Caretaker