G'day
I am modelling a complex of two proteins, each of which has moderately high sequence similarity to their respective template proteins. I wish to create a model that strongly resembles their targets. The idea being that I wish to demonstrate the plausibility of the interface between the two template proteins being conserved in the target proteins. What is the best way to go about this? Presently, I have created a number of models using the library_schedule autosched.fastest with a starting coordinate deviation of zero (i.e. no random displacement added to the initial set of coordinates) and taken the best scoring of these. Is there a better way that optimizes the MODELLER score, but that does not stray far from the template structure, particularly in the ungapped, high similarity regions?
Kind regards,
Rob Jorissen Ludwig Institute for Cancer Research, Melbourne branch
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