BinBin - this is an even tougher question !

On Sun, 28 Mar 2004 13:10:07 +0100 Binbin Liu bmbbl@bmb.leeds.ac.uk wrote:

> 100 models were generated based on one template. Their atomic RMSDs > all are less than 0.4 Angstroms. Does any body know any other way I > can find a representative model from the 100 models.

The low variation in RMSD is an indicator that you gave Modeller a good set of alignments and templates to work with. From your last email, this variation seems appropriate for an essentially well determined backbone with an ensemble of different side-chain conformations. What you do now all depends on what the model is for.

If you have some biochemical criteria (ligand binding, metal ion site conservation, etc), then you would want the model that has the right conformation for the protein's function. This can be quite hard to do if you don't really know what conformation is necessary for function, though!

If you just want to pick the most likely model, and you do not have any more information, then all that you can do is trust in statistics, and molecular mechanics. The modeller objective function is one guide to quality (as mentioned by Ben and Erick in another posting "Re: OBJECTIVE FUNCTION"). Sort all the models by energy and look at the lowest energy models (see the second line of each structure file to get the energy).

The alternative is to assess the structural quality of each model using a tool like Procheck:

http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html

You could apply this to each model and pick the one which has the best quality, based on all the Procheck analysis'. There is also a very easy to use analysis program called ERRAT, available from here : http://www.doe-mbi.ucla.edu/Services/ERRAT/

Hope this helps,

j. _______________________________________________________________________ Dr JB Procter:Biomolecular Modelling at ZBH - Center for Bioinformatics Hamburg http://www.zbh.uni-hamburg.de/staff.php