[MMTK] Using MMTK for protein structure prediction

Siamak Ravanbakhsh mravanba at ualberta.ca
Fri Oct 8 19:53:30 UTC 2010

Hi everyone,

I'm looking for a toolbox that enables me to evaluate an idea in protein structure prediction. I've been trying to figure out if MMTK is the right toolbox. A simple model e.g. c-alpha, is good enough but I need access to individual energy terms. I'm aware of the energyTerms() method of Universe class here but I need more detailed version including the value for each term in summations (e.g. corresponding to every bond).
Can I play with source code to get this, or is it easier/possible for me to calculate the terms for a given configuration myself?

Another question is: 
How can I produce different configurations by sampling a bounded range of possible values for all phi, psi and bond lengths (as they are my optimization variables and I need to calculate the energy corresponding to a set of samples coming from a distribution over these variables)?

If you think this is not the right tool, do you have any suggestion of what other toolbox is available that better fits my needs?

Any help is appreciated.


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